Insulin-like growth factor binding protein 7 for treatment of cancer

ABSTRACT

Methods of treating a tumor in a subject include identifying a subject having, at risk for, or suspected of having a tumor, and administering to the subject an effective amount of an IGFBP7 agent if the tumor has increased Ras-BRAF-MEK-Erk signaling, is dependent for growth and/or survival upon the Ras-BRAF-MEK-Erk signaling pathway, and/or expresses an activated or oncogenic BRAF or RAS.

This application is a continuation of U.S. application Ser. No.12/209,028, filed on Sep. 11, 2008, which claims the benefit of U.S.Provisional Patent Application Ser. No. 60/993,211, filed on Sep. 11,2007, and U.S. Provisional Patent Application Ser. No. 61/092,230, filedon Aug. 27, 2008. The entire contents of the prior applications areincorporated by reference herein.

TECHNICAL FIELD

This invention relates to treatment of cancers with agents that includea polypeptide.

BACKGROUND

Activating V-Raf murine sarcoma viral oncogene homolog B1 (BRAF)mutations are prevalent in numerous types of cancers, including 50-70%of melanomas, 15% of colorectal and ovarian cancers, and 36-69% ofpapillary thyroid carcinomas (reviewed in Davies et al., 2002, Nature,417:949-954; and Namba et al., 2003, J. Clin. Endocr. Metab.,88:4393-97). Activating BRAF mutations have also been identified in upto 82% of benign melanocytic tumors (nevi) (Pollock et al., 2003, NatureGenet., 33:19-20). The most common activating BRAF mutation is aglutamic acid to valine substitution at position 600 (V600E; formerlyidentified as V599E). This mutation produces a highly active kinase thatstimulates constitutive extracellular signal-regulated protein kinase(ERK) signaling. Expression of BRAFV600E has been shown to inducesenescence in cultured human fibroblasts (Zhu et al., 1998, Genes Dev.,12:2997-3007) and human melanocytes (Michaloglou et al., 2005, Nature,436:720-724) and in vivo in preneoplastic nevi (Michaloglou et al.,2005, Nature, 436:720-724).

SUMMARY

This disclosure is based, in part, on the surprising discovery thatinsulin-like growth factor binding protein 7 (IGFBP7) induces senescenceand/or apoptosis in cells with increased Ras-BRAF-MEK-Erk signaling,e.g., cells that express activated forms of BRAF or a RAS viral oncogenehomolog (RAS) (e.g., neuroblastoma RAS viral oncogene homolog (NRAS),V-KI-RAS2 Kirsten rat sarcoma viral oncogene homolog (KRAS), or V-HA-RASHarvey rat sarcoma viral oncogene homolog (HRAS)). Described herein aremethods of diagnosing and treating tumors (e.g., cancers), inducingcellular apoptosis, inducing cellular senescence, and inhibitingcellular proliferation using IGFBP7 agents.

In one aspect, this application features methods of treating a tumor ina subject by identifying a subject having, at risk for, or suspected ofhaving a tumor; and administering to the subject an effective amount ofan IGFBP7 agent, thereby treating the tumor. In some embodiments, thetumor is a cancer (e.g., a melanoma, carcinoma, breast cancer, ovariancancer, pancreatic cancer, colorectal carcinoma, or papillary thyroidcarcinoma). In some embodiments, the tumor has increasedRas-BRAF-MEK-Erk signaling. In some embodiments, the tumor is dependentfor growth and/or survival upon the Ras-BRAF-MEK-Erk signaling pathway.In some embodiments, the tumor expresses an activated or oncogenic BRAFor RAS (e.g., NRAS, KRAS, or HRAS). In some embodiments, the activatedor oncogenic BRAF has a valine to glutamine mutation at residue 600(BRAFV600E).

In some embodiments, the methods further include evaluating a samplefrom the subject to determine the presence of increased Ras-BRAF-MEK-Erksignaling, dependence for growth and/or survival upon theRas-BRAF-MEK-Erk signaling pathway, and/or an activated or oncogenicBRAF or RAS, and selecting the subject for treatment on the basis of thepresence of the increased Ras-BRAF-MEK-Erk signaling, dependence forgrowth and/or survival upon the Ras-BRAF-MEK-Erk signaling pathway,and/or activated or oncogenic BRAF or RAS. In some embodiments, thesample includes a cell, nucleic acid, or polypeptide from the tumor. Insome embodiments, the activated or oncogenic BRAF has a valine toglutamine mutation at residue 600 (BRAFV600E).

In another aspect, this application features methods of inducingsenescence in a cell (e.g., a tumor cell) that has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or expresses an activated oroncogenic BRAF or RAS (e.g., NRAS, KRAS, or HRAS) that includeadministering to the cell an effective amount of an IGFBP7 agent. Insome embodiments, the cell is a tumor cell.

In a further aspect, this application features methods of inducingapoptosis in a cell (e.g., a tumor cell) that has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or expresses an activated oroncogenic BRAF or RAS (e.g., NRAS, KRAS, or HRAS) that includeadministering to the cell an effective amount of an IGFBP7 agent.

In another aspect, this application features methods of inhibitingproliferation of a cell (e.g., a tumor cell) that has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or expresses activated oroncogenic BRAF or RAS (e.g., NRAS, KRAS, or HRAS), in which the methodsinclude administering to the cell an effective amount of an IGFBP7agent.

In a further aspect, this application features methods of inhibitinggrowth (e.g., metastatic growth) in a subject of a tumor that contains acell that has increased Ras-BRAF-MEK-Erk signaling, is dependent forgrowth and/or survival upon the Ras-BRAF-MEK-Erk signaling pathway,and/or expresses an activated or oncogenic BRAF or RAS (e.g., NRAS,KRAS, or HRAS) that include administering to the subject an effectiveamount of an IGFBP7 agent.

In another aspect, this application features the use of an IGFBP7 agentin the preparation of a medicament for the treatment of a tumor orcancer (e.g., a melanoma, carcinoma, breast cancer, ovarian cancer,pancreatic cancer, colorectal carcinoma, or papillary thyroid carcinoma)in a subject. In some embodiments, the tumor has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or expresses an activatedBRAF or RAS (e.g., NRAS, KRAS, or HRAS). In some embodiments, the tumoror cancer is metastatic.

In a further aspect, this application features an isolated IGFBP7 agentfor treating a tumor or cancer (e.g., a melanoma, carcinoma, breastcancer, ovarian cancer, pancreatic cancer, colorectal carcinoma, orpapillary thyroid carcinoma) in a subject. In some embodiments, thetumor has increased Ras-BRAF-MEK-Erk signaling, is dependent for growthand/or survival upon the Ras-BRAF-MEK-Erk signaling pathway, and/orexpresses an activated BRAF or RAS (e.g., NRAS, KRAS, or HRAS). In someembodiments, the tumor or cancer is metastatic.

In some embodiments, the IGFBP7 agent is a composition that includes apolypeptide at least 80% identical (e.g., at least 85%, 90%, 95%, 98%,or 99% identical) to SEQ ID NO:1 or SEQ ID NO:7. The polypeptide can beconjugated to a heterologous moiety (e.g., a heterologous polypeptidesequence). In some embodiments, the IGFBP7 agent includes a functionalfragment or domain of SEQ ID NO:1 or SEQ ID NO:7. The IGFBP7 agent canbe administered, e.g., topically, systemically, or locally (e.g., by adrug-releasing implant).

In some embodiments, the IGFBP7 agent is administered by introducinginto the subject a composition that induces the expression of IGFBP7 oran active fragment or analog thereof, e.g., a nucleic acid encoding apolypeptide at least 80% identical (e.g., at least 85%, 90%, 95%, 98%,or 99% identical) to SEQ ID NO:1 or SEQ ID NO:7. The nucleic acid can bein a vector, e.g., a viral vector (e.g., an adenovirus vector, anadeno-associated virus vector, a retrovirus vector, or a lentivirusvector). In some embodiments, the IGFBP7 agent is administered byintroducing into the subject a cell that a nucleic acid encoding apolypeptide at least 80% identical (e.g., at least 85%, 90%, 95%, 98%,or 99% identical) to SEQ ID NO:1 or SEQ ID NO:7 that secretes thepolypeptide.

In another aspect, this application features methods of diagnosing alesion (e.g., a melanocytic skin lesion) that include: obtaining asample of a lesion (e.g., a melanocytic skin lesion) (e.g., a tissuesample, cell sample, protein sample, or nucleic acid sample) anddetermining the expression of IGFBP7 in the sample, wherein the lesionis diagnosed as benign (e.g., a melanocytic nevus) if the sampledetectably expresses IGFBP7 and wherein the lesion is diagnosed ascancerous (e.g., a melanoma) if the sample does not express IGFBP7. Insome embodiments, the methods include determining whether the sample hasincreased Ras-BRAF-MEK-Erk signaling, is dependent for growth and/orsurvival upon the Ras-BRAF-MEK-Erk signaling pathway, and/or contains anactivated BRAF or RAS (e.g., BRAFV600E) and diagnosing the lesion asbenign (e.g., a melanocytic nevus) if the sample expresses IGFBP7 andhas increased Ras-BRAF-MEK-Erk signaling, is dependent for growth and/orsurvival upon the Ras-BRAF-MEK-Erk signaling pathway, and/or contains anactivated BRAF or RAS. The lesion is diagnosed as cancerous (e.g., amelanoma) if the sample does not express IGFBP7 and has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or contains an activatedBRAF or RAS. In some embodiments, the methods include determiningwhether the sample has increased Ras-BRAF-MEK-Erk signaling, isdependent for growth and/or survival upon the Ras-BRAF-MEK-Erk signalingpathway, and/or contains an activated BRAF or RAS (e.g., BRAFV600E) anddiagnosing the lesion as benign (e.g., a melanocytic nevus) if thesample expresses IGFBP7 and has increased Ras-BRAF-MEK-Erk signaling, isdependent for growth and/or survival upon the Ras-BRAF-MEK-Erk signalingpathway, and/or contains an activated BRAF or RAS and diagnosing thelesion as cancerous (e.g., a melanoma) if the sample expresses IGFBP7but does not have increased Ras-BRAF-MEK-Erk signaling, is not dependentfor growth and/or survival upon the Ras-BRAF-MEK-Erk signaling pathway,and/or does not contain an activated BRAF or RAS.

“Polypeptide” and “protein” are used interchangeably and mean anypeptide-linked chain of amino acids, regardless of length orpost-translational modification.

As used herein, a subject “at risk of developing cancer” is a subjectthat has a predisposition to develop cancer, i.e., a genetic or familialpredisposition to develop cancer or has been exposed to conditions thatcan result in cancer. From the above it will be clear that subjects “atrisk of developing cancer” are not all subjects.

A subject “suspected of having cancer” is one having one or moresymptoms of cancer. Symptoms of cancer are well-known to those of skillin the art and include, without limitation, weight loss, weakness,excessive fatigue, difficulty eating, loss of appetite, unusual molefeatures, newly pigmented skin area, skin growths, skin ulcers, skinlumps, chronic cough, worsening breathlessness, breathing difficulty,enlarged lymph nodes, coughing up blood, blood in the urine, blood instool, nausea, vomiting, liver metastases, lung metastases, bonemetastases, breast or nipple changes, nipple discharge, abdominalfullness, bloating, fluid in peritoneal cavity, constipation, abdominaldistension, perforation of colon, acute peritonitis (infection, fever,pain), vaginal bleeding, pain, vomiting blood, heavy sweating, fever,high blood pressure, anemia, diarrhea, jaundice, dizziness, chills,muscle spasms, colon metastases, lung metastases, bladder metastases,liver metastases, bone metastases, kidney metastases, pancreasmetastases, difficulty swallowing, and the like. For example, a patientwho has been diagnosed by a physician as having cancer is stillsuspected of having cancer.

The term “cancer” refers to cells having the capacity for autonomousgrowth. Examples of such cells include cells having an abnormal state orcondition characterized by rapidly proliferating cell growth. The termis meant to include cancerous growths, e.g., tumors; oncogenicprocesses, metastatic tissues, and malignantly transformed cells,tissues, or organs, irrespective of histopathologic type or stage ofinvasiveness. Also included are malignancies of the various organsystems, such as respiratory, cardiovascular, renal, reproductive,hematological, neurological, hepatic, gastrointestinal, and endocrinesystems; as well as adenocarcinomas which include malignancies such asmost colon cancers, renal-cell carcinoma, prostate cancer and/ortesticular tumors, non-small cell carcinoma of the lung, cancer of thesmall intestine, and cancer of the esophagus. Cancer that is “naturallyarising” includes any cancer that is not experimentally induced byimplantation of cancer cells into a subject, and includes, for example,spontaneously arising cancer, cancer caused by exposure of a patient toa carcinogen(s), cancer resulting from insertion of a transgeniconcogene or knockout of a tumor suppressor gene, and cancer caused byinfections, e.g., viral infections. The term “carcinoma” is artrecognized and refers to malignancies of epithelial or endocrinetissues.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the present invention, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In case of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples are illustrative only and not intendedto be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1A is a schematic summary of the genome-wide shRNA screen for genesrequired for the BRAFV600E-mediated block to cellular proliferation.

FIG. 1B is a set of representations of photographs depictingproliferation of the 17 BRAFV600E/BJ KD cell lines. 1×10⁴ BJ fibroblastsstably expressing the indicated shRNA were cultured in 12-well plateformat, infected with the BRAFV600E-expressing retrovirus, and after 14days stained with crystal violet. NS, non-silencing control shRNA.

FIG. 1C is a bar graph depicting quantitative proliferation assays ofthe 17 BRAFV600E/melanocyte KD cell lines. BJ fibroblasts stablyexpressing the indicated shRNA were infected with theBRAFV600E-expressing retrovirus and after 14 days analyzed by trypanblue exclusion test. Growth of BRAFV600E/melanocytes is expressedrelative to the growth of normal melanocytes. For theBRAFV600E/melanocyte KD cell lines, values were normalized to the growthof the corresponding melanocyte KD cell line in the absence of BRAFV600Eexpression. Error bars represent standard error.

FIG. 1D is a bar graph depicting DNA replication assays of the 17BRAFV600E/melanocyte KD cell lines. DNA replication was monitored byBrdU incorporation 4 days after BRAFV600E expression.

FIG. 1E is a bar graph depicting apoptosis of the 17BRAFV600E/melanocyte KD cell lines. Apoptosis was monitored by AnnexinV-PE staining 4 days after BRAFV600E expression.

FIG. 1F is a set of immunoblots depicting immunoblot analysis monitoringinduction of p16^(INK4a) and acetylation of histone 3 lysine 9 (H3K9) ineach of the 17 BRAFV600E/melanocyte KD cell lines. β-ACTIN (ACTB) wasmonitored as a loading control.

FIG. 2A (top) is an analysis of IGFBP7 levels in CM from normalmelanocytes, BRAFV600E/melanocytes, BRAFV600E/melanocytes stablyexpressing an IGFBP7 shRNA or in BRAFV600E/melanocyte CM treated with anα-IGFBP7 antibody to immunodeplete IGFBP7.

FIG. 2A (bottom) is a bar graph depicting proliferation of naïvemelanocytes following addition of the different CMs described above.Proliferation was measured 14 days after CM addition and normalized tothe growth of untreated melanocytes. Error bars represent standarderror.

FIG. 2B is a Coomassie-stained gel of purified, recombinant IGFBP7(rIGFBP7). The positions of molecular weight markers are shown on theleft, in kDa.

FIG. 2C is a line graph depicting a proliferation assay monitoring theeffect of rIGFBP7 on the growth of melanocytes 14 days after treatment.

FIG. 2D is a set of twelve micrographs depicting β-galactosidasestaining of melanocytes infected with a retrovirus expressing eitherempty vector (first column) or BRAFV600E (second column), or melanocytestreated with CM from BRAFV600E/melanocytes (third column) or rIGFBP7(fourth column). Images are shown at a magnification of 10×, 20× and40×.

FIG. 2E is a set bar graphs depicting growth rates of untreatedmelanocytes, or melanocytes stably expressing a non-silencing (NS) orIGFBP7 shRNA. Cell number was monitored every day for six days.

FIG. 3A is an immunoblot analysis (top) monitoring expression of IGFBP7in the CM from human melanoma cell lines and an associated bar graph(bottom) showing quantitative real-time RT-PCR analysis of IGFBP7expression of human melanoma cell lines containing either an activatingBRAFV600E mutation (SK-MEL-28, MALME-3M, WM793B, WM39, and WM278), anactivating RASQ61R mutation (SK-MEL-2, SK-MEL-103, and WM1366), or werewild type for both BRAF and RAS (CHL, SK-MEL-31, WM1321, and WM3211).Error bars represent standard error.

FIG. 3B is a bar graph depicting proliferation of human melanoma celllines 24 hours after treatment with rIGFBP7. Proliferation wasnormalized to the growth of the corresponding cell line in the absenceof rIGFBP7 addition. Error bars represent standard error.

FIG. 3C is a bar graph depicting apoptosis of human melanoma cell lines24 hours after treatment with rIGFBP7.

FIG. 3D is a set of immunoblots of expression of SMARCB1, BNIP3L andactivated caspase 3 (act-CASP3) in SK-MEL-28 cells in the presence orabsence of rIGFBP7 and stably expressing either a non-silencing (NS),SMARCB1 or BNIP3L shRNA. β-actin (ACTB) was monitored as a loadingcontrol.

FIG. 3E is a bar graph depicting STAT1 recruitment to the SMARCB1promoter in SK-MEL-28 cells as measured by ChIP analysis.

FIG. 3F is a pair of bar graphs depicting SMARCB1 (left) or STAT1(right) mRNA levels in SK-MEL-28 cells following treatment with an NS orSTAT1 siRNA, as measured by qRT-PCR.

FIG. 3G is a pair of bar graphs depicting SMARCB1 (left) or BRG1 (right)recruitment to the BNIP3L promoter in SK-MEL-28 cells as measured byChIP analysis.

FIG. 3H is a line graph depicting apoptosis of SK-MEL-28 cells.SK-MEL-28 cells were incubated with rIGFBP7 for 0, 2, 6, 12, or 24hours, following which the cells were washed and cultured in mediumlacking rIGFBP7. Apoptosis was then quantitated after 24 hours.

FIG. 4A is a set of immunoblots monitoring levels of phospho-ERK andtotal ERK in SK-MEL-28 cells treated for 24 hours with increasingconcentrations of rIGFBP7 (0.2, 1.0, 2.0, 5.0 or 10 μg/ml).

FIG. 4B is a bar graph depicting sensitivity of SK-MEL-28 cells torIGFBP7. Cells were transfected with an empty expression vector or aconstitutively active ERK2 mutant. Cell growth was analyzed 24 hoursafter treatment with rIGFBP7 and normalized to the growth of thecorresponding cell line in the absence of rIGFBP7 addition. Error barsrepresent standard error.

FIG. 4C is a set of immunoblots monitoring expression of BNIP3L,act-CASP3, phospho-ERK and total ERK in SK-MEL-28 cells stablytransfected with an empty expression vector or a constitutivelyactivated ERK2 mutant. SK-MEL-28 cells were either untreated or treatedwith 10 μg/ml of rIGFBP7, as indicated, for 24 hours prior to harvestingcells.

FIG. 4D is a set of immunoblots monitoring expression of BNIP3L,SMARCB1, act-CASP3, phospho-ERK and total ERK in SK-MEL-28 cells 24hours following treatment with rIGFBP, a MEK inhibitor (MEK-i) or a RAFinhibitor (RAF-i).

FIG. 5A is a line graph depicting tumor volume of xenografted micetreated locally with rIGFBP7. SK-MEL-28 or SK-MEL-31 cells were injectedsubcutaneously into the flanks of nude mice, and three, six, and ninedays later (arrows), the mice were injected at the tumor site withrIGBP7 or, as a control, PBS. Error bars represent standard error.

FIG. 5B is a line graph depicting tumor volume of xenografted micetreated systemically with rIGFBP7. SK-MEL-28 or SK-MEL-31 cells wereinjected into the flanks of nude mice. When tumors reached a size of 100mm³, 100 μg rIGFBP7 was systemically administered by tail vein injectionat days 6, 9, and 12 (arrows).

FIG. 5C is a bar graph depicting dose-dependent suppression of tumorgrowth by rIGFBP7. SK-MEL-28 cells were injected into the flanks of nudemice as described in (FIG. 5B), following which 2, 20, 50, 100, or 250μg rIGFBP7 was systemically administered by tail vein injection. Tumorvolume was measured at day 21 following injection.

FIG. 6A is a set of immunohistochemical slides depicting IGFBP7expression in normal human skin (normal skin—column 1), nevi(BRAFV600E-positive—columns 2 and 3), and melanoma (BRAFV600E—columns 4and 5; and BRAF-wt—columns 6 and 7) samples. Samples were stained withhematoxylin and eosin (H&E) (row 1). Images depicting IGFBP7 expressionare shown at 2× (row 2) and/or 20× (row 3) magnification. Arrowheadsindicate IGFBP7-positive melanocytes in normal skin.

FIG. 6B is a schematic summary of how activated BRAF promotessenescence. In BRAF-wt melanocytes, normal signaling through theBRAF-MEK-ERK pathway leads to induction of IGFBP7, which in turninhibits the BRAF-MEK-ERK pathway through an autocrine/paracrinepathway; the result is controlled proliferation. In BRAFV600E-positivenevi, constitutive activation of the BRAF-MEK-ERK pathway leads toinduction of IGFBP7, which inhibits the pathway and activates senescencegenes. In BRAFV600E-positive melanoma, IGFBP7 expression is lost, andthe cells undergo uncontrolled proliferation. Addition of exogenousIGFBP7 inhibits the BRAF-MEK-ERK pathway and activates apoptosis genes.

FIG. 7A is a polypeptide sequence of human IGFBP7 (SEQ ID NO: 1; GenBankAccession No. NP_(—)001544).

FIG. 7B is a nucleotide sequence of human IGFBP7 mRNA (SEQ ID NO:2;GenBank Accession No. NM_(—)001553).

FIG. 8A is a polypeptide sequence of human BRAF (SEQ ID NO:3; GenBankAccession No. NP_(—)004324).

FIG. 8B is a nucleotide sequence of human BRAF mRNA (SEQ ID NO:4;GenBank Accession No. NM_(—)004333)

FIG. 9A is a polypeptide sequence of human NRAS (SEQ ID NO:5; GenBankAccession No. NP_(—)002515).

FIG. 9B is a nucleotide sequence of human NRAS mRNA (SEQ ID NO:6;GenBank Accession No. NM_(—)002524).

FIG. 10A is a schematic of the IGFBP7 promoter; positions of the CpGdinucleotides are shown to scale by vertical lines.

FIG. 10B is a bisulfite sequence analysis of the IGFBP7 promoter inmelanocytic nevi (BRAFV600E), melanoma (BRAF wt), and melanoma(BRAFV600E). Each circle represents a CpG dinucleotide: open (white)circles denote unmethylated CpG sites and filled (black) circlesindicate methylated CpG sites. Each row represents a single clone.

FIG. 10C is a bisulfite sequence analysis of the IGFBP7 promoter in apanel of the indicated melanoma cell lines. Each circle represents a CpGdinucleotide: open (white) circles denote unmethylated CpG sites andfilled (black) circles indicate methylated CpG sites. Each rowrepresents a single clone.

FIG. 10D is a bar graph depicting IGFBP7 mRNA levels in melanoma celllines following treatment with the DNA methyltransferase inhibitor5-aza-2′-deoxycytidine (5-aza), as measured by qRT-PCR. Error barsrepresent standard error.

FIG. 11A is a bar graph depicting sensitivity of the indicated humancancer cell lines to IGFBP7-mediated apoptosis. RAS/BRAF mutation statusis indicated by the bars, as shown on the legend.

FIG. 11B is a bar graph depicting sensitivity of the indicated humancancer cell lines to growth inhibition by the MEK inhibitor U0216.RAS/BRAF mutation status is indicated by the bars, as shown on thelegend.

FIG. 12A is a schematic diagram of an experimental protocol to determinethe effect of IGFBP7 on metastatic lung tumors in xenografted mice.

FIGS. 12B and 12C are a pair of representations of photographs of miceshowing concentrations of GFP-expressing cells in vivo at day sixfollowing injection with A375 (Fluc-IRES-GFP) cells. FIG. 12B,PBS-control treated; FIG. 12C, IGFBP7 treated.

FIG. 12D is a chart depicting Kaplan-Meier analysis of survival of miceover the course of the experiment.

FIG. 13A is a schematic diagram of an experimental protocol to determinethe effect of IGFBP7 on metastatic lung tumors in xenografted mice.

FIG. 13B is a chart depicting Kaplan-Meier analysis of survival of miceover the course of the experiment.

DETAILED DESCRIPTION

This disclosure includes methods of treating tumors (e.g., cancers),inducing cellular apoptosis, inducing cellular senescence, andinhibiting cellular proliferation with IGFBP7 agents.

IGFBP7 Agents

IGFBP7 agents that can be used with the methods described herein areagents that include an IGFBP7 polypeptide sequence and, alternatively,one or more polypeptide or non-polypeptide moieties, such that the agenthas at least 25% (e.g., at least: 30%; 40%; 50%; 60%; 70%; 75%; 80%;85%; 90%; 95%; 97%; 98%; 99%; 99.5%, or 100% or even greater) of theability of rIGFBP7 (see Example 1) to inhibit the proliferation of humanBJ primary foreskin fibroblasts in vitro. Exemplary agents includefragments and analogs of IGFBP7 (see below). The IGFBP7 polypeptidesequence can include a mature, soluble IGFBP7 polypeptide (e.g.,residues 24 to 282, 25 to 282, 26 to 282, 27 to 282, 28 to 282, or 29 to282 of SEQ ID NO:1), one or more domains of IGFBP7, or fragments orvariants thereof. Exemplary fragments of IGFBP7 include the sequencefrom residues 84 to 103 of SEQ ID NO:1 (GMECVKSRKRRKGKAGAAAG; SEQ IDNO:7).

In certain embodiments, IGFBP7 polypeptides include sequencessubstantially identical to all or a portion of a naturally occurringIGFBP7 polypeptide. Polypeptides “substantially identical” to the IGFBP7polypeptide sequence described herein have an amino acid sequence thatis at least 65% (e.g., at least 75%, 80%, 85%, 90%, 95%, 98%, or 99%,e.g., 100%), identical to the amino acid sequences of the IGFBP7polypeptide represented by SEQ ID NO:1 or SEQ ID NO:7. Furthermore, anIGFBP7 polypeptide with up to 50, e.g., 1, 3, 5, 10, 15, 20, 25, 30, or40, amino acid insertions, deletions, or substitutions, e.g.,conservative amino acid substitutions will be useful in the compositionsand methods described herein. A “conservative amino acid substitution”is one in which the amino acid residue is replaced with an amino acidresidue having a similar side chain. Families of amino acid residueshaving similar side chains have been defined in the art. These familiesinclude amino acids with basic side chains (e.g., lysine, arginine,histidine), acidic side chains (e.g., aspartic acid, glutamic acid),uncharged polar side chains (e.g., glycine, asparagine, glutamine,serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g.,alanine, valine, leucine, isoleucine, proline, phenylalanine,methionine, tryptophan), beta-branched side chains (e.g., threonine,valine, isoleucine) and aromatic side chains (e.g., tyrosine,phenylalanine, tryptophan, histidine).

The percent identity between two amino acid sequences can be determinedusing the BLAST 2.0 program, which is available to the public atncbi.nlm.nih.gov/BLAST. Sequence comparison is performed using thedefault parameters (BLOSUM 62 matrix, gap existence cost of 11, perresidue gap cost of 1, and a lambda ratio of 0.85). The mathematicalalgorithm used in BLAST programs is described in Altschul et al., 1997,Nucleic Acids Research, 25:3389-3402.

IGFBP7 polypeptides useful in the methods described herein can be, butare not limited to, recombinant polypeptides and naturally occurringpolypeptides. An IGFBP7 polypeptide can be obtained from any human ormammalian species, and include alternatively spliced forms and otherisoforms that have the disclosed activities. Non-human IGFBP7polypeptides with similarity to human IGFBP7 polypeptides have beenidentified in chimpanzees (e.g., GenBank Accession No. XP_(—)517274),rhesus monkeys (e.g., GenBank Accession Nos. XP_(—)001083041,XP_(—)001082658), cattle (e.g., GenBank Accession No. XP_(—)873466),dogs (e.g., GenBank Accession Nos. XP_(—)850270, XP_(—)861128), mice(e.g., GenBank Accession No. Q61581), and rats (e.g., GenBank AccessionNo. NP_(—)001013066).

Also useful in the new methods are fusion proteins in which a portion ofan IGFBP7 polypeptide is fused to an unrelated polypeptide (e.g., amarker polypeptide or purification tag) to create a fusion protein. Forexample, the polypeptide can be fused to a peptide tag to facilitatepurification (e.g., a hexa-histidine tag or a FLAG tag to facilitatepurification of bacterially expressed polypeptides or to a hemagglutinintag or a FLAG tag to facilitate purification of polypeptides expressedin eukaryotic cells). Also useful are, for example, polypeptides thatinclude a first portion and a second portion; the first portionincludes, e.g., an IGFBP7 polypeptide, and the second portion includes,e.g., a detectable marker or a serum protein, e.g., an immunoglobulinconstant region, or human serum albumin.

The amino-terminal region of IGFBP7 (up to residue 81 of SEQ ID NO:1)contains a region having homology with other insulin-like growth factorbinding proteins (IGFBPs). This region includes conserved cysteineresidues at residues 32, 35, 40, 48, 57, 59, 60, 63, 71, and 81 and aconserved “GCGCCxxC” domain at residues 56 to 63 (see Kim et al., 1997,Proc. Natl. Acad. Sci. 94:12981-86). Other conserved domains of IGFBP7include a Kazal-type serine protease inhibitors and follistatin-likedomain at about residues 118 to 156 (Conserved Domain Database AccessionNo. cd00104) and an immunoglobulin domain, cell adhesion moleculesubfamily, at about residues 160-162 to 248 (Conserved Domain DatabaseAccession No. cd00931). Conserved residues and domains can be used whenproducing fragments, analogs, and variants of IGFBP7 polypeptides.

An IGFBP7 agent can have one or more chemical modifications (e.g.,posttranslational modifications) at one or more sites on thepolypeptide, e.g., at the amino or carboxy terminus. Methods of chemicalmodification are well-known to those of skill in the art, and can beused to alter one or more properties, e.g., activity, stability,retention, or pharmacokinetics of the IGFBP7 agent. Exemplarymodifications include glycosylation and PEGylation. IGFBP7 contains aputative N-glycosylation site at residues 171 to 173 of SEQ ID NO:1.Pegylation of IGFBP4 is described in US 2006/0100144. Similarmodifications and methods can be used with IGFBP7 agents.

An IGFBP7 agent can also be a peptidomimemtic version of a IGFBP7polypeptide (e.g., SEQ ID NO:1 or SEQ ID NO:7), functional fragment, orvariant thereof. These polypeptides can be modified according to themethods known in the art for producing peptidomimetics. See, e.g.,Kazmierski, W. M., ed., Peptidomimetics Protocols, Human Press (TotowaN.J. 1998); Goodman et al., eds., Houben-Weyl Methods of OrganicChemistry: Synthesis of Peptides and Peptidomimetics, Thiele Verlag (NewYork 2003); and Mayo et al., J. Biol. Chem., 278:45746 (2003). In somecases, these modified peptidomimetic versions of the peptides andfragments disclosed herein exhibit enhanced stability in vivo, relativeto the non-peptidomimetic peptides.

Methods for creating a peptidomimetic include substituting one or more,e.g., all, of the amino acids in a peptide sequence with D-amino acidenantiomers. Such sequences are referred to herein as “retro” sequences.In another method, the N-terminal to C-terminal order of the amino acidresidues is reversed, such that the order of amino acid residues fromthe N-terminus to the C-terminus of the original peptide becomes theorder of amino acid residues from the C-terminus to the N-terminus inthe modified peptidomimetic. Such sequences can be referred to as“inverso” sequences.

Peptidomimetics can be both the retro and inverso versions, i.e., the“retro-inverso” version of a peptide disclosed herein. The newpeptidomimetics can be composed of D-amino acids arranged so that theorder of amino acid residues from the N-terminus to the C-terminus inthe peptidomimetic corresponds to the order of amino acid residues fromthe C-terminus to the N-terminus in the original peptide.

Other methods for making a peptidomimetics include replacing one or moreamino acid residues in a peptide with a chemically distinct butrecognized functional analog of the amino acid, i.e., an artificialamino acid analog. Artificial amino acid analogs include β-amino acids,β-substituted β-amino acids (“β³-amino acids”), phosphorous analogs ofamino acids, such as amino phosphonic acids and amino phosphinic acids,and amino acids having non-peptide linkages. Artificial amino acids canbe used to create peptidomimetics, such as peptoid oligomers (e.g.,peptoid amide or ester analogues), β-peptides, cyclic peptides,oligourea or oligocarbamate peptides; or heterocyclic ring molecules.

Also useful in the methods disclosed herein are nucleic acid moleculesthat encode IGFBP7 agents described herein, e.g., naturally occurringIGFBP7 polypeptides or forms of IGFBP7 polypeptides in which naturallyoccurring amino acid sequences are altered or deleted (e.g., fragmentsor analogs of IGFBP7). Certain nucleic acids can encode polypeptidesthat are soluble under normal physiological conditions. IGFBP7 agentscan be expressed (e.g., exogenously expressed) within a cell by anymeans known in the art. To generate cells that express IGFBP7 agents,the cells can be transfected, transformed, or transduced using any of avariety of techniques known in the art. Any number of transfection,transformation, and transduction protocols known to those in the art maybe used, for example those outlined in Current Protocols in MolecularBiology, John Wiley & Sons, New York. N.Y., or in numerous kitsavailable commercially (e.g., Invitrogen Life Technologies, Carlsbad,Calif.). Such techniques may result in stable or transienttransformants. One suitable transfection technique is electroporation,which can be performed on a variety of cell types, including mammaliancells, yeast cells and bacteria, using commercially available equipment.Optimal conditions for electroporation (including voltage, resistanceand pulse length) are experimentally determined for the particular hostcell type, and general guidelines for optimizing electroporation can beobtained from manufacturers.

Exemplary methods of administering IGFBP7 agents include introducinginto a subject a nucleic acid that encodes an IGFBP7 agent describedherein. In some embodiments, the nucleic acid that encodes the IGFBP7agent is contained within a vector, e.g., as a virus that includes anucleic acid that expresses the IGFBP7 agent. Exemplary viral vectorsinclude adenoviruses (reviewed in Altaras et al., 2005, Adv. Biochem.Eng. Biotechnol., 99:193-260), adeno-associated viruses (reviewed inPark et al., 2008, Front. Biosci., 13:2653-59; see also Williams, 2007,Mol. Ther., 15:2053-54), parvoviruses, lentiviruses, retroviruses(reviewed in Tai et al., 2008, Front. Biosci., 13:3083-95), and theherpes simplex virus. Method of delivery of nucleic acids are reviewedin Patil et al., 2005, AAPS J., 7:E61-77, which is incorporated hereinby reference in its entirety.

In some embodiments, a nucleic acid that expresses an IGFBP7 polypeptideis administered directly to cancer cells or to cells in the vicinity ofthe cancer cells. In some embodiments, a nucleic acid that expresses anIGFBP7 polypeptide is administered to a cell ex vivo, which is thenadministered to the subject in the vicinity of the tumor.

An IGFBP7 agent can be produced by any means known in the art, e.g., bychemical synthesis, recombinant methods, or isolation from cells thatnaturally produce IGFBP7. Methods of purification and isolation ofmolecules that include polypeptides are also well known to those ofskill in the art. An exemplary method of purifying IGFBP7 from culturedcells is described in Yamauchi et al., 1994, Biochem J., 303:591-598.

Production of Fragments and Analogs of IGFBP7

Generation of Fragments

Fragments of a protein can be produced in several ways, e.g.,recombinantly, by proteolytic digestion, or by chemical synthesis.Internal or terminal fragments of a polypeptide can be generated byremoving one or more nucleotides from one end (for a terminal fragment)or both ends (for an internal fragment) of a nucleic acid that encodesthe polypeptide. Expression of the mutagenized DNA produces polypeptidefragments. Digestion with “end-nibbling” endonucleases can thus generateDNAs that encode an array of fragments. DNAs that encode fragments of aprotein can also be generated by random shearing, restriction digestionor a combination of the above-discussed methods.

Fragments can also be chemically synthesized using techniques known inthe art such as conventional Merrifield solid phase f-Moc or t-Bocchemistry. For example, peptides of the present invention can bearbitrarily divided into fragments of desired length with no overlap ofthe fragments, or divided into overlapping fragments of a desiredlength.

Generation of Analogs: Production of Altered DNA and Peptide Sequencesby Random Methods

Amino acid sequence variants of a protein can be prepared by randommutagenesis of DNA which encodes a protein or a particular domain orregion of a protein. Useful methods include PCR mutagenesis andsaturation mutagenesis. A library of random amino acid sequence variantscan also be generated by the synthesis of a set of degenerateoligonucleotide sequences. (Methods for screening proteins in a libraryof variants are elsewhere herein.)

PCR Mutagenesis

In PCR mutagenesis, reduced Taq polymerase fidelity is used to introducerandom mutations into a cloned fragment of DNA (Leung et al., 1989,Technique 1:11-15). This is a very powerful and relatively rapid methodof introducing random mutations. The DNA region to be mutagenized isamplified using the polymerase chain reaction (PCR) under conditionsthat reduce the fidelity of DNA synthesis by Taq DNA polymerase, e.g.,by using a dGTP/dATP ratio of five and adding Mn²⁺ to the PCR reaction.The pool of amplified DNA fragments are inserted into appropriatecloning vectors to provide random mutant libraries.

Saturation Mutagenesis

Saturation mutagenesis allows for the rapid introduction of a largenumber of single base substitutions into cloned DNA fragments (Mayers etal., 1985, Science 229:242). This technique includes generation ofmutations, e.g., by chemical treatment or irradiation of single-strandedDNA in vitro, and synthesis of a complimentary DNA strand. The mutationfrequency can be modulated by modulating the severity of the treatment,and essentially all possible base substitutions can be obtained. Becausethis procedure does not involve a genetic selection for mutant fragmentsboth neutral substitutions, as well as those that alter function, areobtained. The distribution of point mutations is not biased towardconserved sequence elements.

Degenerate Oligonucleotides

A library of homologs can also be generated from a set of degenerateoligonucleotide sequences. Chemical synthesis of a degenerate sequencescan be carried out in an automatic DNA synthesizer, and the syntheticgenes then ligated into an appropriate expression vector. The synthesisof degenerate oligonucleotides is known in the art (see for example,Narang, SA (1983) Tetrahedron 39:3; Itakura et al. (1981) RecombinantDNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. AG Walton,Amsterdam: Elsevier pp 273-289; Itakura et al. (1984) Annu. Rev.Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al.(1983) Nucleic Acid Res. 11:477. Such techniques have been employed inthe directed evolution of other proteins (see, for example, Scott et al.(1990) Science 249:386-390; Roberts et al. (1992) PNAS 89:2429-2433;Devlin et al. (1990) Science 249: 404-406; Cwirla et al. (1990) PNAS 87:6378-6382; as well as U.S. Pat. Nos. 5,223,409, 5,198,346, and5,096,815).

Generation of Analogs: Production of Altered DNA and Peptide Sequencesby Directed Mutagenesis

Non-random or directed, mutagenesis techniques can be used to providespecific sequences or mutations in specific regions. These techniquescan be used to create variants that include, e.g., deletions,insertions, or substitutions, of residues of the known amino acidsequence of a protein. The sites for mutation can be modifiedindividually or in series, e.g., by (1) substituting first withconserved amino acids and then with more radical choices depending uponresults achieved, (2) deleting the target residue, or (3) insertingresidues of the same or a different class adjacent to the located site,or combinations of options 1-3.

Alanine Scanning Mutagenesis

Alanine scanning mutagenesis is a useful method for identification ofcertain residues or regions of the desired protein that are preferredlocations or domains for mutagenesis, Cunningham and Wells (Science244:1081-1085, 1989). In alanine scanning, a residue or group of targetresidues are identified (e.g., charged residues such as Arg, Asp, H is,Lys, and Glu) and replaced by a neutral or negatively charged amino acid(most preferably alanine or polyalanine). Replacement of an amino acidcan affect the interaction of the amino acids with the surroundingaqueous environment in or outside the cell. Those domains demonstratingfunctional sensitivity to the substitutions are then refined byintroducing further or other variants at or for the sites ofsubstitution. Thus, while the site for introducing an amino acidsequence variation is predetermined, the nature of the mutation per seneed not be predetermined. For example, to optimize the performance of amutation at a given site, alanine scanning or random mutagenesis can beconducted at the target codon or region and the expressed desiredprotein subunit variants are screened for the optimal combination ofdesired activity.

Oligonucleotide-Mediated Mutagenesis

Oligonucleotide-mediated mutagenesis is a useful method for preparingsubstitution, deletion, and insertion variants of DNA, see, e.g.,Adelman et al., (DNA 2:183, 1983). Briefly, the desired DNA is alteredby hybridizing an oligonucleotide encoding a mutation to a DNA template,where the template is the single-stranded form of a plasmid orbacteriophage containing the unaltered or native DNA sequence of thedesired protein. After hybridization, a DNA polymerase is used tosynthesize an entire second complementary strand of the template thatwill thus incorporate the oligonucleotide primer, and will code for theselected alteration in the desired protein DNA. Generally,oligonucleotides of at least 25 nucleotides in length are used. Anoptimal oligonucleotide will have 12 to 15 nucleotides that arecompletely complementary to the template on either side of thenucleotide(s) coding for the mutation. This ensures that theoligonucleotide will hybridize properly to the single-stranded DNAtemplate molecule. The oligonucleotides are readily synthesized usingtechniques known in the art such as that described by Crea et al. (Proc.Natl. Acad. Sci. (1978) USA, 75: 5765).

Cassette Mutagenesis

Another method for preparing variants, cassette mutagenesis, is based onthe technique described by Wells et al. (Gene (1985) 34:315). Thestarting material is a plasmid (or other vector) that includes theprotein subunit DNA to be mutated. The codon(s) in the protein subunitDNA to be mutated are identified. There must be a unique restrictionendonuclease site on each side of the identified mutation site(s). If nosuch restriction sites exist, they can be generated using theabove-described oligonucleotide-mediated mutagenesis method to introducethem at appropriate locations in the desired protein subunit DNA. Afterthe restriction sites have been introduced into the plasmid, the plasmidis cut at these sites to linearize it. A double-stranded oligonucleotideencoding the sequence of the DNA between the restriction sites butcontaining the desired mutation(s) is synthesized using standardprocedures. The two strands are synthesized separately and thenhybridized together using standard techniques. This double-strandedoligonucleotide is referred to as the cassette. This cassette isdesigned to have 3′ and 5′ ends that are comparable with the ends of thelinearized plasmid, such that it can be directly ligated to the plasmid.This plasmid now contains the mutated desired protein subunit DNAsequence.

Combinatorial Mutagenesis

Combinatorial mutagenesis can also be used to generate mutants. Forexample, the amino acid sequences for a group of homologs or otherrelated proteins are aligned, preferably to promote the highest homologypossible. All of the amino acids that appear at a given position of thealigned sequences can be selected to create a degenerate set ofcombinatorial sequences. The variegated library of variants is generatedby combinatorial mutagenesis at the nucleic acid level, and is encodedby a variegated gene library. For example, a mixture of syntheticoligonucleotides can be enzymatically ligated into gene sequences suchthat the degenerate set of potential sequences are expressible asindividual peptides, or alternatively, as a set of larger fusionproteins containing the set of degenerate sequences.

Primary High-Through-Put Methods for Screening Libraries of PeptideFragments or Homologs

Various techniques are known in the art for screening generated mutantgene products. Techniques for screening large gene libraries ofteninclude cloning the gene library into replicable expression vectors,transforming appropriate cells with the resulting library of vectors,and expressing the genes under conditions in which detection of adesired activity, e.g., inhibition of human BJ proliferation, ismeasured. Each of the techniques described below is amenable to highthrough-put analysis for screening large numbers of sequences created,e.g., by random mutagenesis techniques.

Activating Mutations

The methods and compositions described herein are particularly useful inthe treatment of cancers that include cells that have increasedRas-BRAF-MEK-Erk signaling, are dependent for growth and/or survivalupon the Ras-BRAF-MEK-Erk signaling pathway, and/or have activatingmutations in the BRAF signal transduction pathway (e.g., activating BRAFor RAS (e.g., NRAS, HRAS, or KRAS)) (see, e.g., Dhomen and Marais, 2007,Curr. Opin. Genet. Dev., 17:31-39). BRAF activates the MAP kinaseextracellular signal regulated kinase (MEK), which in turnphosphorylates and activates extracellular signal-regulated kinases 1and 2 (ERK1 and ERK2). Activating BRAF mutations have been found in amajority of melanoma samples tested, as well as in samples from severalother types of cancers. Activating RAS mutations have been found inseveral cancers, including melanoma, multiple myeloma, colorectalcancer, follicular carcinoma, follicular adenoma, leukemia, breastcancer, ovarian cancer, gastric cancer, lung cancer, bladder cancer,pancreatic cancer, lung adenocarcinoma, gall bladder cancer, bile ductcancer, thyroid cancer, and various carcinomas.

An increase in Ras-BRAF-MEK-Erk signaling in a cell can be measured,e.g., by detecting the presence of phosphorylated forms of theseproteins in the cell or a cell lysate. Antibodies specific forphosphorylated BRAF, MEK and Erk are commercially available, e.g., fromCell Signaling Technology, Inc. (Danvers, Mass.) and Santa CruzBiotechnology, Inc. (Santa Cruz, Calif.).

A cell that is dependent for growth and/or survival upon theRas-BRAF-MEK-Erk signaling pathway will display reduced growth and/orsurvival when the expression or activity of a component of theRas-BRAF-MEK-Erk pathway is artificially inhibited, e.g., bypharmacologic (e.g., the farnesyltransferase inhibitor R115777, theMEK1/2 inhibitor PD184352, the MEK inhibitor U0216 (Cell Signaling), theMEK inhibitor PD98054 (Calbiochem), the RAF inhibitor GW5074 (Sigma),BAY 43-9006, CI-1040, hypothemycin, or PD0325901) (Solit et al., 2006,Nature, 439:358-362; Alessi et al., 1995, J. Biol. Chem., 270:27489-94)or genetic means (e.g., transfection with dominant-negative Ras, MEK1shRNA, or an inhibitory nucleotide against a component of the pathway).

Activated BRAF proteins have one or more of the following properties:elevated kinase activity, increased signaling to ERK in vivo or invitro, transformation of NIH 3T3 cells, and decreased proliferation ofhuman foreskin fibroblasts (e.g., BJ fibroblasts or primary foreskinfibroblasts). Exemplary activating BRAF point mutations includesubstitution of Val600 with Glu (V600E; caused by, e.g., a T→Atransversion at nucleotide 1799 of the BRAF coding sequence),substitution of Arg462 with Ile (R462I; caused by, e.g., a G→Ttransversion at nucleotide 1385 of the BRAF coding sequence),substitution of Ile463 with Ser (1463S; caused by, e.g., a T→Gtransversion at nucleotide 1388 of the BRAF coding sequence),substitution of Gly464 with Glu (G464E; caused by, e.g., a G→Atransition at nucleotide 1391 of the BRAF coding sequence), substitutionof Lys601 with Glu (K601E; caused by, e.g., an A→G transition atnucleotide 1801), substitution of Gly465 with Val (G465V), substitutionof Leu596 with Arg (L596R) or Val (L596V), substitution of Gly468 withArg (G468R) or Ala (G468A), and substitution of Asp593 with Gly (D593G).Activating BRAF mutations caused by chromosomal rearrangements have alsobeen identified. For example, a fusion of the AKAP9 and BRAF proteinshas been reported, caused by an inversion of chromosome 7q, resulting inan in-frame fusion between exons 1-8 of the AKAP9 gene and exons 9-18 ofBRAF (Clampi et al., 2005, J. Clin. Invest., 115:94-101).

Activated RAS proteins have one or more of the following properties:increased signaling to RAF (e.g., BRAF) in vivo or in vitro,transformation of NIH 3T3 cells, and decreased proliferation of humanforeskin fibroblasts (e.g., BJ fibroblasts of primary foreskinfibroblasts). Exemplary activating NRAS point mutations includesubstitution of Gly13 with Arg (G13R, caused by a G→C mutation at codon13) and substitution of Gln61 with Arg (Q61R, caused by a CAA→CGAmutation at codon 61). See also Bos et al., 1985, Nature, 315:726-730;Davis et al., 1984, Cytogenet. Cell Genet., 37:448-449; Taparowsky etal., 1983, Cell, 34:581-586; Yuasa et al., 1984, Proc. Nat. Acad. Sci.USA, 81:3670-74). Exemplary activating HRAS point mutations includesubstitution of Gly12 with Val (G12V, caused by a GGC→GTC mutation atcodon 12) and substitution of Gln61 with Lys (Q61K, caused by a CAG→AAGmutation at codon 61). Exemplary activating KRAS point mutations includesubstitution of Gly12 with Cys (G12C, caused by a G→T transversion atnucleotide 34), substitution of Gly 12 with Arg (G12R, caused by a G→Ctransversion at codon 12), substitution of Gly13 with Asp (G13D, causedby a G→A transition at codon 13), substitution of Ala59 with Thr (A59T,caused by a G→A transition at codon 59), substitution of Gly12 with Asp(G12D), substitution of Gly12 with Val (G12V), substitution of Gly12with Ser (G125, caused by a G→A transition at codon 12), insertion ofGly11 (G11-INS, caused by a 3-bp insertion in exon 1), and substitutionof Gly13 with Arg (G13R, caused by a G→C transversion at codon 13).

Constitutively activated ERK mutants include ERK2Q103A andERK2L73P,S151D (Emrick et al., 2006, Proc. Natl. Acad. Sci. USA,103:18101-06; Emrick et al., 2001, J. Biol. Chem., 276:46469-79). Anexemplary activated MEK1 mutant is MEK1EE (Tournier et al., 1999, Mol.Cell. Biol., 19:1569-81).

Activating BRAF, RAS, ERK, or MEK mutations can be detected by assayingfor the presence of mutant nucleic acids in a sample from the subject.An exemplary, commercially available assay to detect BRAF mutations isthe Mutector® mutation detection kit (Trimgen, Sparks, Md.; Cat. Nos.GP04, MH1001-01, MH1001-02, MH1001-03, MH1001-04) (Xing et al., 2004,Clin. Endocrinol. Metab., 89:2867-72; Ichii-Nakato et al., 2006, J.Invest. Dermatol., 126:2111-18). An exemplary, commercially availableassay to detect KRAS mutations is available from DxS Ltd. (Manchester,UK).

Other exemplary methods of detecting mutant nucleic acids include directsequencing; restriction fragment analysis (Cohen et al., 2003, Invest.Ophthalmol. Vis. Sci., 44:2876-78); single-strand conformationpolymorphism gel electrophoresis (Lee et al., 2003, Br. J. Cancer.,89:1958-60); site-directed mutagenesis/restriction analysis (Alsina etal., 2003, Clin. Cancer Res., 9:6419-25; Goydos et al., 2005, J. Am.Coll. Surg., 200:362-370); sequence-specific PCR (Deng et al., 2004,Clin. Cancer Res., 10:191-195); real-time polymerase chain reaction andmelting curve analysis (Ikenoue et al., 2004, Cancer Genet. Cytogenet.,149:68-71); gap ligase chain reaction (Goldenberg et al., 2004, Mod.Pathol., 17:1386-91); mutant allele specific PCR amplification (MASA)(Lilleberg et al., 2004, Ann. NY Acad. Sci., 1022:250-256; Sapio et al.,2006, Eur. J. Endocrinol., 154:341-348); allele-specific PCR (Burger etal., 2006, Eur. Urol., 50:1102-09); real-time allele-specific PCR (Jarryet al., 2004, Mol. Cell. Probes., 18:349-352; Yancovitz et al., 2007, J.Mol. Diagn., 9:178-183); PCR-restriction fragment length polymorphism(RFLP) analysis (Hayashida et al., 2004, Thyroid, 14:910-915; Chung etal., 2006, Clin. Endocrinol. (Oxf.), 65:660-666); mismatch ligationassay (Busby and Morris, 2005, J. Clin. Pathol., 58:372-375); ligasedetection reaction (Turner et al., 2005, J. Cutan. Pathol., 32:334-339);high-resolution amplicon melting analysis (Willmore-Payne et al., 2005,Hum. Pathol., 36:486-493); denaturant capillary electrophoresis(Hinselwood et al., 2005, Electrophoresis, 26:2553-61); loop-hybridmobility shift assay (Matsukuma et al., 2006, J. Mol. Diagn.,8:504-512); single-base extension analysis (Kann et al., 2006, Clin.Chem., 52:2299-2302); oligonucleotide microarray (Kim et al., 2007, J.Mol. Diagn., 9:55-63); in situ hybridization; in situ amplification; andother known means of detecting nucleotide polymorphisms, e.g., singlenucleotide polymorphisms. See also US 2006/0246476, US 2006/0252041, US2007/0020657, and US 2007/0087350. In some embodiments, the presence orabsence of several mutant nucleic acids is assayed (e.g., sequentiallyor simultaneously).

Activating BRAF, RAS, ERK, or MEK mutations can also be detected byassaying for the presence of mutant proteins. Exemplary methods fordetecting mutant proteins include immunological methods usingmutation-specific antibodies (Fensterle et al., 2004, BMC Cancer, 4:62;Kawakami et al., 2005, Cancer Metastasis Rev., 24:357-66); arrayscontaining mutation-specific antibodies; and mass spectrometry (e.g.,MS/MS or MALDI-TOF mass spectrometry) (Powell et al., 2005, J. Pathol.,205:558-64). In some embodiments, the presence or absence of severalmutant proteins is assayed (e.g., sequentially or simultaneously).

Activating BRAF, RAS, ERK, or MEK mutations can also be detected byassaying a sample for BRAF or RAS activity (see, e.g., US 2006/0211073).Alternatively, the presence of an activating BRAF, RAS, ERK, or MEKmutation can be inferred by detecting a characteristic pattern of geneexpression generated by the mutant protein.

A sample from a subject can be of any type without limitation, includinga biopsy, aspirate, blood, plasma, lymph, urine, saliva, or other bodilyfluid. The sample will often include cells of the subject, e.g., cellsfrom a tumor, lesion, or suspected cancerous tissue of the subject.However, many of the detection methods described herein are sensitiveenough to detect traces of mutant nucleic acids or proteins in acell-free sample, even in the presence of the corresponding wild-typenucleic acids or proteins. A sample containing cells can be fixed orotherwise processed prior to assaying.

Cancer Diagnostics

The diagnosis of certain cancers (e.g., cancers with activated BRAF orRAS) can be accomplished by testing a sample (e.g., one or more cells)from a suspected tumor for expression of IGFBP7. A sample that hasincreased Ras-BRAF-MEK-Erk signaling, is dependent for growth and/orsurvival upon the Ras-BRAF-MEK-Erk signaling pathway, and/or contains anactivated BRAF or RAS and does not substantially or detectably expressIGFBP7 (e.g., as compared to a sample from a non-cancerous cell ortissue from the subject or a reference value (e.g., obtained from normalcell or tissue samples)) is diagnosed as cancerous. Likewise, a samplethat does not have increased Ras-BRAF-MEK-Erk signaling, is notdependent for growth and/or survival upon the Ras-BRAF-MEK-Erk signalingpathway, and/or does not contain an activated BRAF or RAS and does notsubstantially or detectably express IGFBP7 (e.g., as compared to asample from a non-cancerous cell or tissue from the subject or areference value (e.g., obtained from normal cell or tissue samples)) canbe diagnosed as cancerous.

The diagnostic methods described herein can be used for lesions orsuspected tumors of any organ or tissue. When the organ or tissue isskin, the sample can contain melanocytic cells. Melanocytic cells thathave increased Ras-BRAF-MEK-Erk signaling, are dependent for growthand/or survival upon the Ras-BRAF-MEK-Erk signaling pathway, and/orcontain an activated BRAF or RAS and substantially express IGFBP7 arediagnosed as melanocytic nevi (moles); melanocytic cells that haveincreased Ras-BRAF-MEK-Erk signaling, are dependent for growth and/orsurvival upon the Ras-BRAF-MEK-Erk signaling pathway, and/or expressactivated BRAF or RAS, but do not substantially express IGFBP7 arediagnosed as melanoma. Melanocytic cells that do not have increasedRas-BRAF-MEK-Erk signaling, are not dependent for growth and/or survivalupon the Ras-BRAF-MEK-Erk signaling pathway, and/or do not contain anactivated BRAF or RAS but do substantially or detectably express IGFBP7are also diagnosed as melanoma. The assays can be used with tissuesections (e.g., frozen tissue sections), and are therefore useful forhistological analysis and clinical diagnosis. The methods do not requirea particular method of tissue fixation, as the assay works with unfixedcells or tissue or with several kinds of fixatives, e.g.,methanol/acetone fixation, or formaldehyde fixation. The assay can workwith paraffin sections, e.g., renatured paraffin sections. Other usefultissue fixation methods are known to one of ordinary skill in the art.

Methods for detecting expression of IGFBP7 in a sample include detectingmRNA or cDNA and detecting protein, e.g., using an antibody or otherbinding protein, or using an activity assay. It is also possible todetect IGFBP7 mRNA or cDNA using any of a variety of moleculartechniques, including RT-PCR and microarray analysis.

Examples of methods of gene expression analysis known in the art includeDNA arrays or microarrays (Brazma and Vilo, FEBS Lett., 2000, 480,17-24; Celis et al., FEBS Lett., 2000, 480, 2-16), SAGE (serial analysisof gene expression) (Madden et al., Drug Discov. Today, 2000, 5,415-425), READS (restriction enzyme amplification of digested cDNAs)(Prashar and Weissman, Methods Enzymol., 1999, 303, 258-72), TOGA (totalgene expression analysis) (Sutcliffe et al., Proc. Natl. Acad. Sci. USA,2000, 97, 1976-81), protein arrays and proteomics (Celis et al., FEBSLett., 2000, 480, 2-16; Jungblut et al., Electrophoresis, 1999, 20,2100-10), expressed sequence tag (EST) sequencing (Celis et al., FEBSLett., 2000, 480, 2-16; Larsson et al., J. Biotechnol., 2000, 80,143-57), subtractive RNA fingerprinting (SuRF) (Fuchs et al., Anal.Biochem., 2000, 286, 91-98; Larson et al., Cytometry, 2000, 41,203-208), subtractive cloning, differential display (DD) (Jurecic andBelmont, Curr. Opin. Microbiol., 2000, 3, 316-21), comparative genomichybridization (Carulli et al., J. Cell Biochem. Suppl., 1998, 31,286-96), FISH (fluorescent in situ hybridization) techniques (Going andGusterson, Eur. J. Cancer, 1999, 35, 1895-904) and mass spectrometrymethods (reviewed in To, Comb. Chem. High Throughput Screen, 2000, 3,235-41).

Cancers

The new methods can be used to diagnose and treat several types ofcancer, e.g., melanomas, thyroid cancers (e.g., papillary thyroidcarcinoma, anaplastic thyroid carcinoma, follicular carcinoma,follicular adenoma), colorectal cancers, lung cancers (e.g.,adenocarcinoma, nonsmall cell lung cancer), lymphomas (e.g., non-Hodgkinlymphoma), multiple myeloma, leukemias, breast cancers, ovarian cancers,gastric cancers, bladder cancers, pancreatic cancers, gall bladdercancers, bile duct cancers, and other carcinomas. Methods of diagnosingcancers are well known to those of skill in the art. In someembodiments, the new methods can be useful for any type of tumor,cancer, or neoplasm that has increased Ras-BRAF-MEK-Erk signaling, isdependent for growth and/or survival upon the Ras-BRAF-MEK-Erk signalingpathway, and/or contains an activated or oncogenic BRAF or RAS.

Pharmaceutical Formulations

The IGFBP7 agents described herein (all of which can be referred toherein as “active compounds”), can be incorporated into pharmaceuticalcompositions. Such compositions typically include the active compoundand a pharmaceutically acceptable carrier or excipient. A“pharmaceutically acceptable carrier” can include solvents, dispersionmedia, coatings, antibacterial and antifungal agents, isotonic andabsorption delaying agents, and the like, compatible with pharmaceuticaladministration. Supplementary active compounds can also be incorporatedinto the compositions.

There are a number of methods by which the new compositions for use inthe new methods can be delivered to subjects, in general, and tospecific cells or tissue in those subjects, in particular. For example,an IGFBP7 agent described herein can be injected into a subject or atissue of the subject. In another example, a vector (e.g., a plasmid orvirus) encoding an IGFBP7 agent can be introduced into a cell or tissueof the subject. The vector would then enter the cell or cells in thattissue and express the IGFBP7 agent. Delivery specificity of suchplasmids can be enhanced by associating them with organ- ortissue-specific affinity, so that they preferentially enter specifiedcell types. However, because IGFBP7 can act extracellularly, it is notnecessary to deliver the vector directly to tumor cells. The vector canbe delivered to the tissue surrounding the tumor. Methods of expressingproteins for tumor therapy are described, e.g., in Cross and Burmester,2006, Clin. Med. Res., 4:218-227; Lejuene et al., 2007, Expert Rev.Anticancer Ther. 7:701-713; and Bloquel et al., 2004, J. Gene Med.,6:S11-S23.

Compounds and their physiologically acceptable salts and solvates can beformulated for oral, topical, buccal, parenteral or rectaladministration or administration by inhalation or insufflation (eitherthrough the mouth or the nose).

The compounds will generally be formulated for parenteral administrationby injection, for example, by bolus injection or continuous infusion.Formulations for injection can be presented in unit dosage form, forexample, in ampoules or in multi-dose containers, with an addedpreservative. The compositions can take such forms as suspensions,solutions or emulsions in oily or aqueous vehicles, and can containformulatory agents such as suspending, stabilizing and/or dispersingagents. Alternatively, the active ingredient can be in powder form forconstitution with a suitable vehicle, for example, sterile pyrogen-freewater, before use. Where the compositions are intended for use in aspecific treatment area, the compositions can be administered by one ormore local injections into the tumor site to diminish as much aspossible any side effects relating to the compound's activities outsideof the treatment area.

In addition to the formulations described previously, the compounds canalso be formulated as a depot preparation. Such long acting formulationscan be administered by implantation (for example subcutaneously orintramuscularly) or by intramuscular injection. Thus, for example, thecompounds can be formulated with suitable polymeric or hydrophobicmaterials (for example as an emulsion in an acceptable oil) or ionexchange resins, or as sparingly soluble derivatives, for example, as asparingly soluble salt. A depot preparation can include embedded orencapsulated cells or tissue that secrete an IGFBP7 agent, which can beadministered, e.g., by implantation or by intramuscular injection.

The compositions can, if desired, be presented in a pack or dispenserdevice that can contain one or more unit dosage forms containing theactive ingredient. The pack can, for example, include metal or plasticfoil, such as a blister pack. The pack or dispenser device can beaccompanied by instructions for administration.

The therapeutic compositions of the invention can also contain a carrieror excipient, many of which are known to skilled artisans. Methods formaking such formulations are well known and can be found in, forexample, Remington: The Science and Practice of Pharmacy, University ofthe Sciences in Philadelphia (USIP), 2005.

The compositions can also be formulated for intracellular delivery ofthe active compounds, using methods known in the art. For example, thecompositions can include liposomes or other carriers that deliver theactive compound across the plasma membrane. Vesicles that are coveredwith membrane-permeant peptides, such as Tat or Antennapedia, can alsobe used. A number of other methods for enhancing intracellular deliveryare familiar to those of skill in the art.

It is recognized that the pharmaceutical compositions and methodsdescribed herein can be used independently or in combination with oneanother. That is, subjects can be administered one or more of thepharmaceutical compositions, e.g., pharmaceutical compositions thatinclude an IGFBP7 agent, subjected to one or more of the therapeuticmethods described herein, or both, in temporally overlapping ornon-overlapping regimens. When therapies overlap temporally, thetherapies can generally occur in any order and can be simultaneous(e.g., administered simultaneously together in a composite compositionor simultaneously but as separate compositions) or interspersed. By wayof example, a subject afflicted with a disorder described herein can besimultaneously or sequentially administered both a cytotoxic agent whichselectively kills aberrant cells and an antibody (e.g., an antibody ofthe invention) which can, in one embodiment, be conjugated or linkedwith a therapeutic agent, a cytotoxic agent, an imaging agent, or thelike.

Effective Doses

Toxicity and therapeutic efficacy of an IGFBP7 agent can be determinedby standard pharmaceutical procedures, using either cells in culture orexperimental animals to determine the LD50 (the dose lethal to 50% ofthe population) and the ED50 (the dose therapeutically effective in 50%of the population). The dose ratio between toxic and therapeutic effectsis the therapeutic index and it can be expressed as the ratio LD50/ED50.Inhibitors that exhibit large therapeutic indices are preferred. Whileinhibitors that exhibit toxic side effects can be used, care can betaken to design a delivery system that targets such compounds to thesite of affected tissue to minimize potential damage to non-target cellsand, thereby, reduce side effects.

The data obtained from the cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofsuch compounds lies preferably within a range of circulatingconcentrations that include the ED50 with little or no toxicity. Thedosage can vary within this range depending upon the dosage formemployed and the route of administration utilized. For any compound usedin the new methods, the therapeutically effective dose can be estimatedinitially from cell culture assays. A dose can also be calculated inanimal models to achieve a circulating plasma concentration range thatincludes the IC50 (that is, the concentration of the test compound whichachieves a half-maximal inhibition of symptoms) as determined in cellculture. Such information can be used to more accurately determineuseful doses in humans.

EXAMPLES Materials and Methods

Cell Lines and Culture

Primary foreskin fibroblasts (BJ) and human melanoma cell lines wereobtained from ATCC and grown in Dulbecco's modified Eagle's mediumsupplemented with 10% fetal calf serum at 37° C. under 5% CO₂. Humanprimary melanocytes were obtained from Cascade Biologics and grown asper the supplier's recommendation.

Retroviruses and Plasmids

Retroviruses expressing empty vector or BRAFV600E were generated fromplasmids pBABE-zeo (Addgene) and pBABE-zeo/BRAFV600E (Michaloglou etal., 2005, Nature, 436:720-724). Plasmids expressing constitutivelyactivated ERK2 mutants ERK2Q103A and ERK2L73P,S151D (Emrick et al.,2006, Proc. Natl. Acad. Sci. USA, 103:18101-06; Emrick et al., 2001, J.Biol. Chem., 276:46469-79) and MEK1 mutant MEK1EE (Tournier et al.,1999, Mol. Cell. Biol., 19:1569-81) were also obtained.

shRNA Screen

The human shRNA^(mir) library (release 1.20; Open Biosystems) wasobtained through the University of Massachusetts Medical School shRNAlibrary core facility. Ten retroviral pools, each comprising ˜6000 shRNAclones, were generated with titers of ˜2.6×10⁵ pfu/ml. These retroviralstocks were produced following co-transfection into the PhoenixGP™packaging cell line (Grignani, 1998, Cancer Res., 58:14-19). PFFfibroblasts (1.2×10⁶) were transduced at an MOI of 0.2 with theretroviral stocks in 100 mm plates, and 2 days later were selected forresistance to puromycin (1.5 μg/ml) for 7 days. Cells were then infectedwith a retrovirus carrying BRAFV600E under conditions in which all cellswere infected (MOI 20). Cells that bypassed the BRAFV600E-inducedcellular proliferation block formed colonies, which were pooled andexpanded, and the shRNAs identified by sequence analysis. To identifythe candidate shRNAs, the shRNA region of the transduced virus was PCRamplified (using primers PSM2-forward, 5′-GCTCGCTTCGGCAGCACATATAC-3′(SEQ ID NO:8) and PSM2-reverse, 5′-GAGACGTGCTACTTCCATTTGTC-3′ (SEQ IDNO:9)) and cloned into pGEM-T Easy (Promega). An average of 48 cloneswere sequenced per pool (using primer PSM2-seq,5′-GAGGGCCTATTTCCCATGAT-3′ (SEQ ID NO:10)). Individual PFF or melanocyteknockdown cell lines were generated by stable transduction of 6×10⁴cells with single shRNAs directed against the candidate gene, followedby infection with the BRAFV600E-expressing retrovirus. Individual shRNAswere either obtained from the Open Biosystems library or synthesized.

Quantitive Real-Time RT-PCR

Total RNA was isolated using TRIZOL™ (Invitrogen) 7 days afterretroviral transduction and puromycin selection. Reverse transcriptionwas performed using SuperScript™ II Reverse Transcriptase (Invitrogen)as per the manufacturer's instructions, followed by quantitativereal-time PCR using Platinum SYBR™ Green qPCR SuperMix-UDG with Rox(Invitrogen).

Proliferation Assay

For the proliferation assay shown in FIG. 1B, 1×10⁴ cells stablyexpressing an shRNA were cultured in 12-well plate format, infected withBRAFV600E-expressing retrovirus and after 14 days stained with crystalviolet. For all other quantitative proliferation assays, cell viabilitywas measured by trypan blue exclusion test at the time point indicatedin the relevant figure legend. Values were expressed as percent cellgrowth, as described in the relevant figure legend. For theproliferation assays shown in FIG. 2A, CM was replenished every 3 days,and proliferation was measured after a total of 14 days of CM treatment.Unless otherwise stated, rIGFBP7 was added to the culture medium at aconcentration of 10 μg/ml.

Apoptosis Assay

PFF fibroblasts or melanocytes or shRNA knockdown derivatives (5×10⁵cells) were infected with BRAFV600E-expressing retrovirus, and 4 dayslater the total cell population was stained for Annexin V-PE (BDBiosciences). To monitor apoptosis in melanoma cells following rIGFBP7treatment, 5×10⁵ cells were treated with rIGFBP7 (10 μg/ml) for 24 hoursand stained for Annexin V-PE.

DNA Replication Assay

PFF fibroblasts or melanocytes or shRNA knockdown derivatives (5×10⁵cells) were infected with BRAFV600E-expressing retrovirus, and ˜4 dayslater the total cell population was stained for BrdU incorporation.Briefly, 4 hours prior to the end of the 4-day infection withBRAFV600E-expressing retrovirus, cells were incubated with 20 μM BrdU(Sigma) to allow for BrdU incorporation, at which point cells were fixedin 70% ethanol, permeabilized using 0.2% Triton™ X-100, treated with 2NHCl, and probed using an a-BrdU antibody (Ab-3, Oncogene) which was thendetected using an anti-mouse IgG Texas Red-conjugated antibody(Calbiochem).

Antibodies and Immunoblot Analysis

To prepare cell extracts, cells were lysed in Laemmli buffer; forphospho-proteins, cells were lysed in the presence of a phosphataseinhibitor cocktail (Sigma). To prepare conditioned media, cells weregrown in Opti-MEM™ (Invitrogen) for 24 hours, and media was harvestedand concentrated using Centricon™ plus 20 tubes (Millipore). Conditionedmedia was normalized to cell number prior to loading the gel. For theexperiments shown in FIGS. 3D and 4C, rIGFBP7 was added to the culturemedium at a concentration of 10 μg/ml. For the MEK/RAF inhibitorexperiment of FIG. 4D, SK-MEL-28 cells were treated with 2 μg/ml or 10μg/ml rIGFBP7, 20 μM or 40 μM of the MEK inhibitor PD98054 (Calbiochem),or 5 nM or 10 nM the RAF inhibitor GW5074 (Sigma) for 24 hours prior toharvesting cells. Proteins were resolved by SDS-PAGE and transferred tonitrocellulose. Blots were probed with the following antibodies: α-p16(Abcam), α-acetylated H3K9 (Upstate), α-IGFBP7 (Santa Cruz), α-SMARCB1(Abnova), α-BNIP3L (Proscience), α-BRAFV600E (Santa Cruz), α-cleavedcaspase-3 p11 (Santa Cruz), α-β-actin (Sigma), α-phospho-ERK (CellSignaling) or α-ERK (Cell Signaling).

Recombinant IGFBP7 Expression and Purification

The human IGFBP7 expression vector pFASTBAC-1/IGFBP7, expressing aC-terminal Flag-tagged fusion protein (Oh, et al., 1996, J. Biol. Chem.,271:30322-25), was used to generate recombinant baculovirus using theBac-to-Bac™ Baculovirus Expression System (Invitrogen) as per themanufacturer's instructions. The recombinant baculovirus construct wasthen transfected into Sf9 cells (Invitrogen) for baculovirus production,and amplified to produce recombinant IGFBP7 protein. Conditioned mediafrom IGFBP7-expressing Sf9 cells was collected and incubated with α-FlagM2 beads (Sigma), and the bound protein was eluted using an α-Flagpeptide.

Senescence-Associated β-Galactosidase Assay

Melanocytes infected with a retrovirus expressing either vector orBRAFV600E, or melanocytes treated with BRAFV600E/melanocyte CM orrIGFBP7 (10 μg/ml) for 14 days were washed twice with PBS (5 minutes atroom temperature), fixed with 3% formaldehyde (5 minutes at roomtemperature), and washed three more times with PBS. Cells were thenincubated at 37° C. (0% CO₂) overnight in SA-β-Gal stain solution (1mg/mL X-Gal (5-bromo-4-chloro-3-indoyl b-D-galactoside), 40 mM citricacid/sodium phosphate (pH 6.0), 5 mM potassium ferrocyanide, 5 mMpotassium ferricyanide, 150 mM NaCl and 2 mM MgCl₂). Cells were washedwith PBS and visualized on a Zeiss Axiovert™ 40 CFL microscope. Imageswere captured using QCapture™ Pro version 5 software (QImagingCorporation).

ChIP Assays

Chromatin immunoprecipitation (ChIP) assays were performed usingextracts prepared 24 hours following rIGFBP7 treatment. The followingantibodies were used: α-BRG1 (de La Serna et al., 2000, Mol. Cell.Biol., 20:2839-51), α-phospho-STAT1 (Upstate), and α-SMARCB1 and α-STAT1(Santa Cruz). For ChIP experiments on the SMARCB1 promoter, primersspanning a STAT1 binding site located ˜2.4 kb upstream of thetranscription start-site were used. For ChIP experiments on the BNIP3Lpromoter, a series of primer-pairs that covered ˜2 kb of the BNIP3Lpromoter were used; following addition of rIGFBP7, SMARCB1 and BRG1 wererecruited to the BNIP3L promoter near the transcription start-site. ChIPproducts were analyzed by quantitative real-time PCR using PlatinumSYBR™ Green qPCR SuperMix-UDG with Rox (Invitrogen). Calculation of folddifferences was done as previously described (Pfaffl, 2001, NucleicAcids Res., 29:e45).

Tumor Formation Assays

5×10⁶ SK-MEL-28 or SK-MEL-31 cells were suspended in 100 μl ofserum-free DMEM and injected subcutaneously into the right flank ofathymic Balb/c (nu/nu) mice (Taconic). Three, six, and nine days later,the mice were injected at the tumor site with either 20 μg of rIGBP7 ina total volume of 100 μl or, as a control, PBS. Tumor dimensions weremeasured every three days and tumor volume was calculated using theformula π/6×(length)×(width)². For the systemic administrationexperiments, 5×10⁶ SK-MEL-28 or SK-MEL-31 cells were injected into theflanks of nude mice and when tumors reached a size of 100 mm3, 100 μgrIGFBP7 in a total volume of 100 μl was delivered by tail vein injectionat days 6, 9, and 12. Tumor dimensions were measured every three days.Animal experiments were performed in accordance with the InstitutionalAnimal Care and Use Committee (IACUC) guidelines.

Immunohistochemistry

The study was approved by the UMass Medical Center institutional reviewboard. Archival materials from normal skin (n=5), nevi (n=20) andmalignant melanoma (primary (n=7) and metastatic (n=13)) were retrievedfrom the pathology files of UMass Medical Center, Worcester, Mass. Thehistologic sections of all cases were re-reviewed and the diagnosesconfirmed by a dermatopathologist. All patient data were de-identified.

Five-micron thick sections were cut for immunohistochemical studies,which were performed using standard techniques with heat-induced epitoperetrieval buffer and primary antibodies against IGFBP7 (1:20 dilution;Santa Cruz). Appropriate positive and negative controls were included.Positive staining was noted by ascertaining expression of IGFBP7 in thecytoplasm. Significant nuclear staining was not noted. All stainedslides were reviewed by the dermatopathologist. Genomic DNA forgenotyping was isolated from ten 10 μm-thick sections using ISS buffer(20× SSC pH 7.0, 3 M NaCl, 0.3 M sodium citrate, 1M NaCl, and 10% SDS)plus 40 μl/ml of 20 mg/ml proteinase K and 4 μl/ml of 0.1 M DTT.Briefly, tissue samples were scraped from the slides and incubated inISS buffer with proteinase K and DTT overnight at 61° C. The followingday, samples were extracted twice with phenol-chloroform, the secondround using Phase Lock Gel (Eppendorf), and the samples were thenprecipitated using ethanol. Genomic DNA was quantitated and itsintegrity checked by gel electrophoresis, followed by PCR amplificationand TA cloning (Promega). Multiple clones were sequenced for identifyingthe V600E mutation (T1796A) in exon 15 of the BRAF gene (primers:Forward primer: 5′-TCATAATGCTTGCTCTGATAGGA-3′ (SEQ ID NO:11), Reverseprimer: 5′-GGCCAAAATTTAATCAGTGGA-3′ (SEQ ID NO:12)).

Bisulfite Sequencing

Bisulfite modification was carried out essentially as described (Frommeret al., 1992, Proc. Natl. Acad. Sci. USA, 89:1827-31), except thathydroquinone was used at a concentration of 125 mM during bisulfitetreatment (carried out in the dark) and DNA was desalted on QIAQUICK™columns (Qiagen) after the bisulfite reaction. Six clones were sequencedfor each cell line or human tissue sample. For 5-aza-2′-deoxycytidine(5-aza) treatment, melanoma cell lines were treated with 10 μM 5-aza(Calbiochem) for 48 hours.

Example 1 A Genome-Wide shRNA Screen Identifies Factors Required forBRAFV600E-Mediated Senescence and Apoptosis

To identify genes required for BRAFV600E to block proliferation ofprimary cells, a genome-wide small hairpin RNA (shRNA) screen wasperformed (shown schematically in FIG. 1A). The primary screen wasperformed in human primary foreskin fibroblasts (PFFs). A human shRNAlibrary comprising ˜62,400 shRNAs directed against 28,000 genes wasdivided into 10 pools, which were packaged into retrovirus particles andused to stably transduce PFFs. The cells were then infected with aretrovirus expressing BRAFV600E under conditions in which all cells wereinfected. Cells that bypassed the BRAFV600E-mediated cellularproliferation block formed colonies, which were pooled and expanded, andthe shRNAs were identified by sequence analysis. Positive candidateswere confirmed by stable transduction of PFFs with single shRNAsdirected against the candidate genes, infection with theBRAFV600E-expressing retrovirus, and quantitation of cellularproliferation. Confirmed candidate shRNAs were then tested in asecondary screen for their ability to bypass the proliferation block inBRAFV600E-expressing primary human melanocytes.

The screen identified 17 genes that, following shRNA-mediated knockdown,enabled BRAFV600E-expressing PFFs (BRAFV600E-PFFs) and melanocytes(BRAFV600E-melanocytes) to proliferate. These genes are listed in Table1, and proliferation assays of the 17 BRAFV600E-PFF knockdown (KD) celllines are shown in FIG. 1B. As expected from previous studies (Zhu etal., 1998, Genes Dev., 12:2997-3007), expression of BRAFV600E in PFFsfor in PFFs containing a control non-silencing (NS) shRNA(BRAFV600E-PFF-NS) efficiently inhibited cellular proliferation (FIG.1B). Significantly, however, this block was overcome in all 17BRAFV600E-PFF KD cell lines. Quantitative real-time RT-PCR (qRT-PCR)confirmed in all cases that expression of the target gene was decreasedin the corresponding PFF and melanocyte KD cell lines. For all 17 genes,a second, unrelated shRNA directed against the same target gene alsoenabled PFFs to proliferate following BRAFV600E expression.

TABLE 1 Genes required for BRAFV600E-induced block to cellularproliferation BIOLOGICAL ACCESSION GENE PROCESS NUMBER SYMBOL NAMEApoptosis NM_004331 BNIP3L BCL2/adenovirus E1B 19 kDa interactingprotein 3-like Cell cycle NM_004336 BUB1 budding uninhibited bybenzimidazoles 1 regulation homolog (yeast) Signal NM_004305 BIN1bridging integrator 1 transduction NM_004134 HSPA9 heat shock 70 kDaprotein 9 (mortalin) NM_001553 IGFBP7 insulin-like growth factor bindingprotein 7 NM_000877 IL1R1 interleukin 1 receptor, type 1 NM_003768 PEA15phosphoprotein enriched in astrocytes 15 NM_002885 RAP1GAP RAP1 GTPaseactivating protein Transcription NM_021145 DMTF1 cyclin D bindingmyb-like transcription regulation factor 1 NM_004496 FOXA1 Forkhead boxA1 NM_002198 IRF1 interferon regulatory factor 1 NM_000244 MEN1 multipleendocrine neoplasia 1 NM_000546 TP53 tumor protein p53 (Li-Fraumenisyndrome) Chromatin NM_001007468 SMARCB1 SWI/SNF related, matrixassociated, actin remodeling dependent regulator of chromatin, subfamilyb, member 1 NM_003325 HIRA HIR histone cell cycle regulation defectivehomolog A (S. cerevisiae) Genome stability NM_000268 NF2 neurofibromin 2(bilateral acoustic neuroma) Unknown NM_024735 FBXO31 F-box protein 31

As expected from previous studies (Michaloglou et al., 2005, Nature,436:720-724), expression of BRAFV600E in primary melanocytes efficientlyblocked cellular proliferation (FIG. 1C). By contrast, BRAFV600E failedto block cellular proliferation in all 17 melanocyte KD cell lines.Thus, the 17 genes we identified are required for BRAFV600E to blockproliferation of both PFFs and primary melanocytes.

Following expression of BRAFV600E in melanocytes, the majority of cellsbecame senescent (FIG. 1D), consistent with previous studies(Michaloglou et al., 2005, Nature, 436:720-724), although ˜10% of cellsunderwent apoptosis (FIG. 1E). To determine the role of the 17 genes inthese two pathways, apoptosis and senescence assays were performed ineach melanocyte KD cell line following BRAFV600E expression. The resultsof FIG. 1E show that only three of the 17 genes were required forapoptosis: BNIP3L, which encodes a pro-apoptotic BCL2 family protein;SMARCB1, which encodes a component of the SWI/SNF chromatin remodelingcomplex; and insulin growth factor binding protein 7 (IGFBP7), whichencodes a secreted protein with weak homology to IGF binding proteins.By contrast, all but one of the 17 genes, BNIP3L, were required forBRAFV600E to induce growth arrest (FIG. 1D) and characteristic markersof senescence (see below). Identical results were obtained in PFFs.

The cell cycle inhibitor p16^(INk4a) has been proposed to play animportant role in replicative and oncogene-induced senescence (reviewedin Ben-Porath and Weinberg, 2005, Int. J. Biochem. Cell Biol.,37:961-976). For example, p16^(INK4a) is induced in melanocytesfollowing expression of activated BRAF, is expressed in melanocyticnevi, and is frequently deleted in melanomas (Michaloglou et al., 2005,Nature, 436:720-724; Piccinin et al., 1997, Int. J. Cancer, 74:26-30).It was therefore determined whether the genes identified in our screenwere required for p16^(INK4a) induction. FIG. 1F shows that p16^(INK4a)levels increased substantially following BRAFV600E expression in controlmelanocytes expressing a non-silencing shRNA. Significantly, p16^(INK4a)expression was not induced by BRAFV600E in 16 of the 17 melanocyte KDcell lines. The sole exception was the cell line knocked down forBNIP3L, which, as described above, is specifically involved inapoptosis. Loss of histone H3 lysine 9 (H3K9) acetylation, another wellcharacterized senescence marker (Narita et al., 2006, Cell,126:503-514), also occurred following BRAFV600E expression in controlmelanocytes, but not in any of the melanocyte KD cell lines except forthe BNIP3L KD cell line (FIG. 1F).

Example 2 A Secreted Protein, IGFBP7, Induces Senescence and Apoptosisthrough an Autocrine/Paracrine Pathway

The 17 genes identified in the screen encoded known tumor suppressors(TP53, MEN1, NF2, and SMARCB1), pro-apoptotic proteins (BNIP3L), cellcycle regulators (BUB1), and modulators of the RAS-RAF-MEK-ERK signalingpathway (PEA15, RAP1GAP, and HSPA9). Unexpectedly, one of the genesrequired for the induction of both senescence and apoptosis was IGFBP7,which encodes a secreted protein (Wilson et al., 1997, J. Clin.Endocrinol. Metab., 82:1301-1303). This result raised the possibilitythat the BRAFV600E-mediated block to cellular proliferation might occurthrough an autocrine/paracrine pathway in which IGFBP7 functionsextracellularly.

To confirm that IGFBP7 is in fact secreted and ask whether IGFBP7functions extracellularly, the ability of conditioned medium (CM) fromBRAFV600E-melanocytes to induce senescence was analyzed. The immunoblotof FIG. 2A (top panel) shows that following expression of BRAFV600E inmelanocytes, the level of IGFBP7 in CM increased substantially. Additionof CM from BRAFV600E-melanocytes to naïve melanocytes blocked cellularproliferation, primarily resulting from the induction of senescence(FIG. 2A, bottom panel and see FIG. 2D below).

Two experiments verified that IGFBP7 activation was downstream ofBRAF-MEK-ERK signaling. First, BRAFV600E-mediated induction of IGFBP7was blocked by addition of a MEK inhibitor. Second, expression of aconstitutively activated ERK mutant (ERK2Q103A or ERK2L73P,S151D) wassufficient to activate IGFBP7 transcription.

The IGFBP7 promoter contains a consensus binding site for the dimericAP-1 (JUN/FOS) transcription factor. JUN (also known as c-Jun) isactivated through RAF-MEK-ERK signaling (Leppa et al., 1998, EMBO J.,17:4404-13), raising the possibility that AP-1 is involved inBRAFV600E-mediated induction of IGFBP7. Chromatin immunoprecipitation(ChIP) analysis verified that JUN bound to the IGFBP7 promoter inresponse to BRAFV600E expression, and siRNA-mediated knockdown of JUNabrogated induction of IGFBP7 transcription in BRAFV600E/melanocytes.

Next, it was verified that IGFBP7 was the secreted protein responsiblefor the BRAFV600E-mediated cellular proliferation block. In oneexperiment, BRAFV600E-melanocytes were treated with an shRNA targetingIGFBP7. FIG. 2A shows that IGFBP7 was absent from the CM ofBRAFV600E-melanocytes expressing an IGFBP7 shRNA (top panel), and thatthis CM did not inhibit cellular proliferation of naïve melanocytes(bottom panel). In a second experiment, immunodepletion with an α-IGFBP7antibody efficiently removed IGFBP7 from CM of BRAFV600E-melanocytes(top panel). Immunodepleted CM also failed to inhibit cellularproliferation of naïve melanocytes (bottom panel).

To confirm that IGFBP7 could block cellular proliferation, purifiedrecombinant IGFBP7 (rIGFBP7) was purified from baculovirus-infectedinsect cells. FIG. 2B shows that following expression and purification,a polypeptide of ˜33 kDa was detected (the expected size of rIGFBP7).Addition of rIGFBP7 blocked proliferation of primary melanocytes in adose-dependent manner (FIG. 2C). The growth-arrested cells had anenlarged, flat morphology and stained positively forsenescence-associated β-galactosidase (FIG. 2D). Collectively, theresults of FIGS. 2A-2D indicate that following expression of BRAFV600E,melanocytes synthesize and secrete increased amounts of IGFBP7, whichthen acts through an autocrine/paracrine pathway to induce senescence.

The finding that primary melanocytes express low levels of IGFBP7 (FIG.2A and see below) raised the possibility that under normal conditionsIGFBP7 might regulate melanocyte proliferation. To test this idea, theproliferation rates of untreated melanocytes, control melanocytesexpressing a non-silencing shRNA, and melanocytes expressing an IGFBP7shRNA were compared. The results of FIG. 2E show that melanocyteproliferation increased following IGFBP7 knockdown. Thus, normalmelanocytes express low levels of IGFBP7, which restrains proliferation.When present at high levels, such as following expression of BRAFV600E,IGFBP7 induces senescence.

Example 3 Selective Sensitivity of Melanoma Cell Lines Containing anActivating BRAF Mutation to IGFBP7-Mediated Apoptosis

Next, the ability of IGFBP7 to block cellular proliferation in a panelof human melanoma cell lines was analyzed. The cells contained either anactivating BRAF mutation (BRAFV600E; SK-MEL-28, MALME-3M, WM793B, WM39and WM278), an activating RAS mutation (RASQ61R; SK-MEL-2, SK-MEL-103,and WM1366), or were wild type for both BRAF and RAS (CHL, SK-MEL-31,WM1321 and WM3211). For each cell line, the presence of IGFBP7 in the CMwas determined by immunoblot analysis (FIG. 3A), and sensitivity toIGFBP7-induced growth inhibition was measured in a proliferation assay(FIG. 3B). The results reveal a striking inverse correlation betweenIGFBP7 expression and sensitivity to IGFBP7-mediated growth inhibitionthat correlates with the status of BRAF or RAS. Most importantly,melanoma cell lines harboring an activating BRAF mutation failed toexpress IGFBP7 and were highly sensitive to IGFBP7-mediated growthinhibition. By contrast, cells with wild type BRAF and RAS expressedIGFBP7 and were relatively insensitive to IGFBP7-mediated growthinhibition. Finally, melanoma cell lines containing an activating RASmutation expressed low levels of IGFBP7 and were partially sensitive toIGFBP7-mediated growth inhibition.

The IGFBP7-mediated cellular proliferation block was further analyzedwith regard to apoptosis and senescence. Significantly, in melanoma celllines harboring an activating BRAF mutation, rIGFBP7 strongly inducedapoptosis and surviving senescent cells were undetectable (FIG. 3C).Thus, IGFBP7 primarily induced senescence in primary melanocytes andapoptosis in BRAFV600E-positive melanoma cells.

To understand the basis of this differential response, expression of the17 identified genes was analyzed in primary melanocytes andBRAFV600E-positive SK-MEL-28 melanoma cells. Quantitative RT-PCR showedthat in primary melanocytes, expression of BRAFV600E resulted in thetranscriptional upregulation of seven genes which are involved inapoptosis (BNIP3L, IGFBP7 and SMARCB1) and senescence (PEA15, IGFBP7,MEN1, FBXO31, SMARCB1, and HSPA9). BRAFV600E-mediated induction of allseven genes did not occur with knockdown of IGFBP7. Following additionof rIGFBP7 to melanocytes, six of the seven genes were induced, IGFBP7being the exception. Significantly, following addition of rIGFBP7 toSK-MEL-28 cells, neither IGFBP7 nor PEA/5 were upregulated. PEA15, aknown regulator of BRAF-MEK-ERK signaling (Formstecher et al., 2001,Dev. Cell, 1:239-250), is required for senescence (see FIG. 1F). Thus,the lack of PEA15 induction in IGFBP7-treated SK-MEL-28 cells canexplain their failure to undergo senescence. BNIP3L is only modestlyupregulated in primary melanocytes following expression of BRAFV600E oraddition of rIGFBP7, consistent with the relatively low level ofapoptosis in IGFBP7-treated melanocytes (see FIG. 1E).

Example 4 IGFBP7 Induces Apoptosis through Upregulation of BNIP3L

As described above, BRAFV600E-mediated apoptosis was dependent uponIGFBP7, SMARCB1, and BNIP3L, raising the possibility that these threeproteins were components of a common pathway required for apoptosis. Aseries of experiments was performed to confirm this idea and establishthe order of the pathway. FIG. 3D shows that following addition ofrIGFBP7 to SK-MEL-28 cells, expression of SMARCB1 and BNIP3L wassignificantly increased, and apoptosis occurred as evidenced by caspase3 activation. Expression of a SMARCB1 shRNA blocked induction of BNIP3Land apoptosis. By contrast, expression of a BNIP3L shRNA still resultedin induction of SMARCB1 following rIGFBP7 addition, although apoptosisdid not occur. Collectively, these results reveal a pathway in whichIGFBP7 increases expression of SMARCB1, which in turn leads to increasedexpression of BNIP3L, culminating in apoptosis (FIG. 3D, bottom panel).

In BRAFV600E/melanocytes, induction of SMARCB1 and BNIP3L was blockedfollowing IGFBP7 knockdown. Moreover, addition of CM fromBRAFV600E-expressing melanocytes to naïve melanocytes substantiallyupregulated SMARCB1 and BNIP3L, which did not occur with various controlCMs that lacked IGFBP7. Thus, in BRAFV600E/melanocytes induction ofSMARCB1 and BNIP3L is also dependent upon and downstream of IGFBP7.

The mechanistic basis for IGFBP7-mediated induction of BNIP3L andSMARCB1 was next determined. STAT1 is involved in certainSMARCB1-inducible transcription responses, and the SMARCB1 promotercontains a STAT1 binding site located ˜2.4 kb upstream of thetranscription start-site (Hartman et al., 2005, Genes Dev., 19:2953-68).The potential role of STAT1 in IGFBP7-mediated induction of SMARCB1transcription was investigated. ChIP experiments revealed that followingaddition of rIGFBP7 to SK-MEL-28 cells, STAT1 was recruited to theSMARCB1 promoter (FIG. 3E), and shRNA-mediated knockdown experimentsconfirmed that STAT1 was required for IGFBP7-mediated upregulation ofSMARCB1 (FIG. 3F).

As described above, SMARCB1 is required for upregulation of BNIP3L byIGFBP7 (FIG. 3D). ChIP experiments revealed that following addition ofrIGFBP7, SMARCB1 as well as BRG1, an essential subunit of the SWI/SNFcomplex (Bultman et al., 2000, Mol. Cell, 6:1287-95), were recruited tothe BNIP3L promoter near the transcription start-site (FIG. 3G).Following knockdown of SMARCB1, BRG1 (and, as expected, SMARCB1) failedto associate with the BNIP3L promoter. Collectively, these resultsindicate that IGFBP7 stimulates BNIP3L transcription, at least in part,by increasing intracellular levels of SMARCB1, leading to formation of aSMARCB1-containing SWI/SNF chromatin-remodeling complex, which isrecruited to the BNIP3L promoter and facilitates BNIP3L transcriptionalactivation.

Finally, it was determined whether apoptosis was dependent upon thecontinual presence of rIGFBP7 or was irreversible following transientexposure to rIGFBP7. SK-MEL-28 cells were incubated with rIGFBP7 forvarious lengths of time, following which the cells were washed andcultured in medium lacking rIGFBP7, and apoptosis was quantitated after24 hours. The results, shown in FIG. 3H, indicate that following 6 hoursof incubation with rIGFBP7, the cells were irreversibly committed toapoptosis, which occurred even following removal of rIGFBP7.

Example 5 IGFBP7 Blocks BRAF-MEK-ERK Signaling to Activate the ApoptoticPathway

As mentioned above, in BRAFV600E-positive melanoma cells BRAF-MEK-ERKsignaling is hyper-activated, rendering the cells highly dependent onthis pathway. Thus, treatment of BRAFV600E-positive melanoma cells witha BRAF shRNA (Hoeflich et al., 2006, Cancer Res., 999-1006) or aninhibitor of BRAF (Sharma et al., 2005, Cancer Res., 65:2412-2421) orMEK (Solit et al., 2006, Nature, 439:358-362) blocks cellularproliferation. It was determined whether IGFBP7 blocks cellularproliferation, at least in part, by inhibiting BRAF-MEK-ERK signaling.

To test this idea, rIGFBP7 was added to BRAFV600E-positive SK-MEL-28melanoma cells, and the levels of total and activated ERK (phospho-ERK)were analyzed. The immunoblot experiment of FIG. 4A shows that additionof rIGFBP7 resulted in a dose-dependent loss of phospho-ERK, indicatingthat BRAF-MEK-ERK signaling was inhibited.

Similarly, expression of BRAFV600E in melanocytes markedly decreasedphospho-ERK levels, which did not occur in BRAFV600E/melanocytesexpressing an IGFBP7 shRNA. Moreover, addition of CM fromBRAFV600E/melanocytes to naïve melanocytes substantially decreased thelevels of phospho-ERK, which did not occur with various control CMs thatlacked IGFBP7. rIGFBP7 also blocked growth factor-induced ERKactivation. Collectively, these results indicate that IGFBP7 inhibitsBRAF-MEK-ERK signaling.

Addition of rIGFBP7 to SK-MEL-28 cells resulted in decreased levels ofactivated MEK1/2, corresponding with the reduced phospho-ERK levels andapoptosis. Moreover, ectopic expression of a constitutively activatedMEK1 mutant (MEK1EE) prevented IGFBP7 from blocking ERK activation.These results demonstrate that IGFBP7 blocks phosphorylation of MEK byBRAF. Finally, addition of IGFBP7 to SK-MEL-28 cells resulted inupregulation of RAF inhibitory protein (RKIP), which has been shown tointeract with several RAF proteins, including BRAF, and inhibitRAF-mediated phosphorylation of MEK (see, for example, Park et al.,2005, Oncogene, 24:3535-40). Following knockdown of RKIP in SK-MEL-28cells, rIGFBP7 failed to block activation of MEK or ERK. Collectively,these results indicate that IGFBP7 inhibits BRAF-MEK-ERK signaling byinducing RKIP, which prevents BRAF from phosphorylating MEK.

To establish the relationship between inhibition of BRAF-MEK-ERKsignaling and the IGFBP7-mediated block to cellular proliferation,sensitivity to rIGFBP7 was analyzed in a constitutively activated ERK2mutant (ERK2Q103A or ERK2L73P,S151D). FIG. 4B shows that expression ofeither ERK2 an ERK2 (left) or MEK1 (right) mutant in SK-MEL-28 cellssubstantially overcame the IGFBP7-mediated cellular proliferation block.Expression of a constitutively activated ERK2 mutant also blockedBRAFV600E- and IGFBP7-induced senescence in melanocytes. In addition,ectopic expression of either constitutively activated ERK2 mutantincreased phospho-ERK2 levels and prevented the IGFBP7-mediatedupregulation of BNIP3L and induction of apoptosis (FIG. 4C).

The above results led to two conclusions. First, IGFBP7 blocked cellularproliferation, at least in part, through inhibition of BRAF-MEK-ERKsignaling. Second, inhibition of BRAF-MEK-ERK signaling was required foractivation of the IGFBP7-mediated apoptotic pathway. FIG. 4D shows thataddition of a chemical inhibitor of MEK or RAF blocked BRAF-MEK-ERKsignaling. However, unlike rIGFBP7, MEK and RAF inhibitors did notincrease BINP3L levels or efficiently induce apoptosis, indicating thatinhibition of BRAF-MEK-ERK signaling is not sufficient to induceIGFBP7-mediated apoptosis. Thus, IGFBP7 has a second, independentactivity required for induction of the apoptotic pathway.

Example 6 IGFBP7 Suppresses Growth of BRAFV600E-Positive Tumors inXenografted Mice

The ability of IGFBP7 to inhibit proliferation of BRAFV600E-positivehuman melanoma cell lines (see FIG. 3B) raised the possibility thatIGFBP7 could suppress growth of tumors containing an activating BRAFmutation. As a first test of this possibility, human melanoma cells thatcontained (SK-MEL-28) or lacked (SK-MEL-31) an activating BRAF mutationwere injected subcutaneously into the flanks of nude mice. Three, six,and nine days later, the mice were injected at the tumor site witheither rIGFBP7 or, as a control, PBS. The results of FIG. 5A show thatrIGFBP7 substantially suppressed growth of BRAFV600E-positive tumors buthad no effect on tumors containing wild type BRAF.

It was also determined whether tumor growth could also be suppressed bysystemic administration of rIGFBP7. SK-MEL-28 or SK-MEL-31 cells wereinjected into the flanks of nude mice, and when tumors reached a size of100 mm³, 100 μg rIGFBP7 was delivered by tail vein injection at days 6,9, and 12. The results of FIG. 5B show that systemic administration ofrIGFBP7 completely suppressed growth of BRAFV600E-positive tumors,whereas tumors containing wild type BRAF were unaffected. In micetreated with rIGFBP7, BRAFV600E-positive tumors were deoxyuridinetriphosphate nick-end labeling (TUNEL)-positive, indicating thatsuppression of tumor growth resulted from apoptosis. Suppression oftumor growth by systemically administered rIGFBP7 was dose-dependent,and concentrations higher than that required for inhibition of tumorgrowth could be delivered without apparent adverse effects (FIG. 5C).

Example 7 Loss of IGFBP7 Expression is Critical for BRAFV600E-PositiveMelanoma

As shown above, BRAFV600E-positive melanoma cell lines fail to expressIGFBP7 and are highly sensitive to IGFBP7-mediated apoptosis. Theseresults raised the possibility that IGFBP7 functions as a tumorsuppressor and loss of IGFBP7 might be required for development ofBRAFV600E-positive melanoma. To investigate this possibility, weperformed immunohistochemical analysis of IGFBP7 expression on a seriesof human skin, nevi, and melanoma samples.

The results of FIG. 6 and Table 2 show that normal skin melanocytesexpressed low but detectable levels of IGFBP7, consistent with theresults in cultured primary melanocytes (see FIG. 2A).BRAFV600E-positive nevi expressed high levels of IGFBP7, consistent withthe finding that expression of BRAFV600E in melanocytes increased IGFBP7levels (FIG. 2A). Significantly, BRAFV600E-positive melanomas did notexpress detectable levels of IGFBP7. By contrast, IGFBP7 was clearlyexpressed in melanomas lacking activated BRAF.

TABLE 2 BRAFV600E and IGFBP7 status in human skin, nevi, and melanomasamples No. of BRAFV600E IGFBP7 Pathology samples status status Normalskin 5 − + Benign nevus 20 + + Melanoma 13 + − Melanoma 7 − +

To determine whether loss of IGFBP7 expression was the result ofepigenetic silencing, bisulfite sequence analysis was performed. FIG.10A shows that the IGFBP7 promoter was densely hypermethylated inBRAFV600E-positive melanomas but not in BRAFV600E-positive nevi ormelanomas lacking activated BRAF. Similar analyses in a panel ofmelanoma cell lines showed that the IGFBP7 promoter was denselyhypermethylated in BRAFV600E-positive melanoma cell lines and modestlyhypermethylated in NRASQ61R-positive melanoma cell lines (FIG. 10B).Treatment of these cell lines with the DNA methyltransferase inhibitor5-aza-2′-deoxycytidine restored IGFBP7 expression in BRAFV600E- andNRASQ61R-positive cell lines but had no effect in BRAF/RAS-wild typecell lines (FIG. 10C).

Collectively, these results suggest that during the development of aBRAFV600E-positive melanoma, IGFBP7 expression is lost (e.g., fromepigenetic silencing involving promoter hypermethylation), enablingescape from the BRAFV600E-mediated senescence that is characteristic ofnevi.

Example 8 A Functional Peptide Derivative of IGFBP7

The inhibitory activity of a peptide derivative of IGFBP7 was assessed.Based on previous observations (Sato et al., 1999, J Cell Biochem. 1999Nov. 1; 75(2):187-95) a 20 amino acid peptide G₈₄MECVKSRKRRKGKAGAAAG₁₀₃(SEQ ID NO:7) was produced. This peptide was tested for its ability toinduce cord-like structures in vascular endothelial cells when assayedas described previously (Akaogi et al., Cell Growth Differ. 1996December; 7(12):1671-7). The 20-amino acid peptide had similar activityto full-length IGFBP7 to induce cord-like structures in vascularendothelial cells.

Example 9 Combined Treatment with IGFBP7 and IDO Inhibitors

Melanoma patients positive for lymphocyte infiltration have betterprognosis, decreased recurrence and almost no metastasis. Advances thatcan improve the immune surveillance in melanoma will have significantimpact on improving the quality of life for the melanoma patients. Themitogen-activated protein kinase (MAPK) pathway is frequently activatedin human melanoma, leading to malignant phenotype such as autonomouscellular proliferation. The screen described above identified a genenamed BIN1 that affects the enzyme indoleamine 2,3-dioxygenase (IDO).IDO catabolizes the first step in tryptophan metabolism, thus depletingthe tryptophan pool on which T-cells depend for their activity. The IDOlevel and lymphocyte infiltration in melanoma samples with BRAFV600E andWT BRAF are analyzed. The use of IDO inhibitors in combination withBRAF-MEK-ERK pathway inhibitors (e.g., IGFBP7 agents described herein)can provide additional effects for treatment of melanoma.

Example 10 Human Cancer Cell Lines are Sensitive to IGFBP7-MediatedApoptosis

The ability of IGFBP7 to induce apoptosis was assessed in the NCI 60panel of human cancer cell lines, which were obtained from the NationalCancer Institute (NCI). The panel includes cell lines corresponding tobreast (MDA-MB-231, HS 578T, 8T-549, T47-D, MCF₇), ovarian (NCI-ADR-RES,OVCAR-3, OVCAR-5, OVCAR-8, OVCAR-4, SK-OV-3, IGROV1), prostate (DU-145,PC-3), renal (TK-10, CAKI-1, A496, ACHN, RXF-393, 786-O, SN12C, UO-31),non-small cell lung (NCI-H460, HOP-62, A549-ATCC, NCI-H226, EKVX,NCI-H322M, HOP-92, NCI-H522), central nervous system (CNS) (SF-295,SF-268, SF-539, SNB-19, SNB-75, U251), colon (HCT-15, SW-620, COLO205,HT29, HCC-2998, HCT-116, SM-12), melanoma (SK-MEL-28, SK-M2L-2, LOXIMVI, M14, MALM-3M, SK-MEL-5, UACC-257, UACC-62, MDA-MB-435), andhematopoietic (CCRF-CEM, K-562, MOLT-4, SR, RPMI-8226) cancers. Thesecell lines have been extensively characterized and their mutationalstatus for a number of human cancer genes, including BRAF and RAS (e.g.,NRAS, KRAS, or HRAS), is known (see the World Wide Web atdiscover.nci.nih.gov/cellminer/mutationGeneLoad.do).

rIGFBP7 was expressed and purified as described above. To monitorapoptosis following rIGFBP7 treatment, 5×10⁵ cells were treated withrIGFBP7 (10 μg/ml) for 24 hours and stained for Annexin V-PE. Theresults are shown in FIG. 11A. rIGFBP7 induced apoptosis in 11/11 (100%)of the cell lines that contained a BRAF mutation and 8/13 (61.5%) of thecell lines that contained a RAS mutation. One cell line contained both aBRAF and a RAS mutation, and this cell line was susceptible torIGFBP7-mediated apoptosis. Of cell lines that did not contain a BRAF orRAS mutation, only 4/34 (11.8%) were susceptible to apoptosis mediatedby rIGFBP7.

The growth dependence of the above cell lines on the Ras-BRAF-MEK-Erksignaling pathway was also determined. 1.5×10⁵ cells of each cell linewere treated with 20 μM of the MEK inhibitor U0216 (Cell Signaling) for24 hours, and growth of the cell lines was determined. The results areshown in FIG. 11B. U0216 inhibited growth in 11/11 (100%) of the celllines that contained a BRAF mutation and 11/13 (84.6) of the cell linesthat contained a RAS mutation. The one cell line that contained both aBRAF and a RAS mutation was susceptible to growth inhibition by U0216.None of the cell lines (0/34) that did not contain a BRAF or RASmutation were susceptible to growth inhibition by U0216.

Example 11 IGFBP7 Suppresses Xenograft Metastasis and Enhances Survival

As a first test of whether IGFBP7 can be used to treat metastaticmelanoma, a well-established mouse model of metastatic disease was usedin which human melanoma cells form pulmonary metastases following tailvein injection (see, for example, Collisson et al., 2003, Cancer Res.,63:5669-73; Hoeflich et al., 2006, Cancer Res., 66:999-1006; Zimmermanet al., 1987, Cancer Res., 47:2305-10). For these experiments,A375(Fluc-IRES-GFP) cells were used, which are a highly metastatic,BRAF-positive human melanoma cell line stably expressing anFluc-IRES-GFP reporter construct (where Fluc is the firefly luciferasegene, IRES is an internal ribosomal entry site and GFP is greenfluorescent protein) (Collisson et al., 2003, Cancer Res.,63:5669-5673). The presence of Fluc-IRES-GFP enables tumor growth to bequantified over time in live animals by serial bioluminescent opticalimaging.

Two treatment regimens were tested. In one set of experiments,administration of IGFBP7 was initiated 3 days after injection ofA375-Fluc cells, at which time metastatic disease would be significant(FIG. 12A). In these experiments, 7×10⁵ A375(Fluc-IRES-GFP) cells wereinjected into the tail vein of 10 athymic Balb/c (nu/nu) mice (Taconic).At days 3, 6 and 9, mice were injected via the tail vein with either 100μg purified, recombinant IGFBP7 (n=5 mice) or, as a control, phosphatebuffered saline (PBS) (n=5 mice). On day 6, mice were analyzed forquantitation of metastatic tumor burden by using a Xenogen brandbioluminescent imaging system. As expected, mice injected with PBSdisplayed metastatic lung tumors (FIG. 12B), whereas mice injected withrIGFBP7 showed no evidence of lung metastasis (FIG. 12C). Mice weremonitored daily for viability over 30 days, and the ability ofsystemically administered IGFBP7 to suppress metastatic disease wasassessed by survival assays (Kaplan-Meier analysis). FIG. 12D shows thatall 5 control mice died at 20 days following injection ofA375(Fluc-IRES-GFP) cells whereas mice injected with rIGFBP7 were stillviable at day 30.

In a second set of experiments, administration of IGFBP7 was initiatedboth before and shortly after injection of A375(Fluc-IRES-GFP) cells, totest the ability of IGFBP7 to function prophylactically to preventmetastasis and/or treat early metastatic disease (FIG. 13A). In theseexperiments, 100 μg purified, recombinant IGFBP7 (or, as a control, PBS)was injected into the tail vein of mice (n=5 mice for each group). Oneday later, mice were injected with 7×10⁵ A375(Fluc-IRES-GFP) cells,followed by injection of 100 μg on days 3 and 6. Mice were monitoreddaily for viability over 30 days, and the ability of systemicallyadministered IGFBP7 to suppress metastatic disease was assessed bysurvival assays (Kaplan-Meier analysis). The results of FIG. 13B showthat mice treated with PBS died within 18 days following injection ofA375(Fluc-IRES-GFP) cells, whereas mice injected with rIGFBP7 were stillviable at day 30. These preliminary results strongly support thepossibility of using rIGFBP7 to treat and prevent metastatic melanoma.

OTHER EMBODIMENTS

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention.Accordingly, other embodiments are within the scope of the followingclaims.

1. A method of treating a tumor in a subject, the method comprising:identifying a subject having, at risk for, or suspected of having atumor; determining that a cell of the tumor has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or expresses an activated oroncogenic BRAF or RAS; and administering to the subject an effectiveamount of an IGFBP7 agent, thereby treating the tumor.
 2. The method ofclaim 1, wherein the tumor is a cancer.
 3. The method of claim 2,wherein the cancer is a melanoma.
 4. The method of claim 2, wherein thecancer is a carcinoma, breast cancer, ovarian cancer, pancreatic cancer,colon cancer, colorectal carcinoma, or papillary thyroid carcinoma. 5.The method of claim 2, wherein the cancer expresses an activated oroncogenic BRAF or RAS.
 6. The method of claim 2, wherein the activatedor oncogenic BRAF is BRAFV600E.
 7. The method of claim 1, wherein theoncogenic BRAF is BRAFV600E.
 8. The method of claim 1, wherein theIGFBP7 agent comprises a polypeptide at least 80% identical to SEQ IDNO:1 or SEQ ID NO:7.
 9. The method of claim 8, wherein the polypeptideis at least 85% identical to SEQ ID NO:1 or SEQ ID NO:7.
 10. The methodof claim 8, wherein the polypeptide is conjugated to a heterologousmoiety.
 11. The method of claim 10, wherein the heterologous moiety is aheterologous polypeptide sequence.
 12. The method of claim 1, whereinthe IGFBP7 agent consists of a polypeptide at least 80% identical to SEQID NO:1 or SEQ ID NO:7.
 13. The method of claim 12, wherein thepolypeptide is at least 85% identical to SEQ ID NO:1 or SEQ ID NO:7. 14.The method of claim 1, wherein the IGFBP7 agent comprises a functionalfragment or domain of SEQ ID NO:1.
 15. The method of claim 1, whereinthe IGFBP7 agent is administered by introducing to the subject a nucleicacid encoding a polypeptide at least 85% identical to SEQ ID NO:1 or SEQID NO:7.
 16. The method of claim 15, wherein the nucleic acid is in aviral vector.
 17. The method of claim 16, wherein the viral vector is anadenovirus, adeno-associated virus, retrovirus, or lentivirus vector.18. The method of claim 1, wherein the IGFBP7 agent is administeredtopically, systemically, or locally.
 19. The method of claim 18, whereinthe IGFBP7 agent is administered locally by a drug-releasing implant.20. A method of inhibiting proliferation of a cell that has increasedRas-BRAF-MEK-Erk signaling, is dependent for growth and/or survival uponthe Ras-BRAF-MEK-Erk signaling pathway, and/or expresses an activated oroncogenic BRAF or RAS, the method comprising administering to the cellan effective amount of an IGFBP7 agent.
 21. The method of claim 20,wherein the cell is a tumor cell. 22-24. (canceled)
 25. A method ofdiagnosing a melanocytic skin lesion, the method comprising: obtaining asample of a melanocytic skin lesion; determining expression of IGFBP7 inthe sample; and determining whether the sample contains an activatedBRAF or RAS; diagnosing the lesion as a melanocytic nevus if the sampleexpresses IGFBP7 and contains an activated BRAF or RAS, diagnosing thelesion as a melanoma if the sample does not express IGFBP7 and containsan activated BRAF or RAS, or diagnosing the lesion as a melanoma if thesample expresses IGFBP7 and does not contain an activated BRAF or RAS.26. The method of claim 25, wherein the sample is a cell.
 27. The methodof claim 25, wherein the expression is mRNA expression.
 28. The methodof claim 25, wherein the expression is protein expression.
 29. A methodof treating a melanoma in a subject, the method comprising: identifyinga subject having, at risk for, or suspected of having a melanoma; andadministering to the subject an effective amount of an IGFBP7 agent,thereby treating the melanoma.
 30. The method of claim 29, wherein theIGFBP7 agent is a composition comprising a polypeptide at least 80%identical to SEQ ID NO:1 or SEQ ID NO:7.